From owner-proteins@net.bio.net Wed Dec 01 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!uunet!biosci!FOX.CCE.USP.BR!szeinfel From: szeinfel@FOX.CCE.USP.BR (Rafael N Szeinfeld) Newsgroups: bionet.molbio.proteins Subject: Magainin 1 (MGN 1) of X.laevis Message-ID: Date: 26 Nov 93 22:50:51 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 13 Hi netters, Could someone direct me to some references that relates the structure of Magainin 1 (produced in skin glangs) of X.laevis with it antimicrobial activity ? Indeed, I tried to retrieve the sequence from swissprot in the hope that a reference would also be sent but I had a negative response, does someone know the accession number of it in any protein database ? Thanks in advance for your help, Rafael Najmanovich szeinfel@fox.cce.usp.br From owner-proteins@net.bio.net Wed Dec 01 22:00:00 1993 Path: biosci!FOX.CCE.USP.BR!mcpalmie From: mcpalmie@FOX.CCE.USP.BR (Mauricio Cesar Palmieri) Newsgroups: bionet.molbio.proteins Subject: looking for proteins sequences Message-ID: Date: 2 Dec 93 11:40:45 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 27 Hi Netters, I have got a protein sequence and I would like to compare it with other ones. Somebody there could tell me some information about how is the easiest manner to proceed a roughly search? (database, software, time required, etc). thanks in advance! ------------------------------------------------------------------------ Mauricio Cesar Palmieri Mestrando em Biotecnologia UNIVERSIDADE DE SAO PAULO BRAZIL E - mail: mcpalmie@fox.cce.usp.br Letters to: Universidade Estadual Paulista Depto. Bioquimica R. Prof Francisco Degni s/n Araraquara - SP - Brazil CEP 14800-900 From owner-proteins@net.bio.net Wed Dec 01 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!spool.mu.edu!agate!ames!purdue!mentor.cc.purdue.edu!aclcb.purdue.edu!MURIANA From: muriana@aclcb.purdue.edu (Peter M. Muriana) Newsgroups: bionet.molbio.proteins Subject: Re: Triton _X-114 Message-ID: Date: 26 Nov 93 15:04:04 GMT References: <2d2pt0$cgp@mserv1.dl.ac.uk> Sender: news@mentor.cc.purdue.edu (USENET News) Reply-To: muriana@aclcb.purdue.edu Distribution: bionet Organization: Purdue University AIDS Center Lines: 30 In article <2d2pt0$cgp@mserv1.dl.ac.uk>, MJ Duggan writes: >Dear Netters, > >Has anybody out there used Triton-X-114 for the phase separation of >membrane proteins ? Michael, I have not, but dusting off my proteins-detergent file I found the following which may be helpful: "Selective release of the Treponema pallidum outer membrane and associated polypeptides with Triton X114" Cunningham et al., J. Bact. 170: 5789, 1988 - they used X114 to release proteins which were distributed between aqueous and hydrophobic phases. In my lab we have used Tween 80 to "float" hydrophobic peptides that associate with it when it flocculates into a surface pellicle in the presence of ammonium sulfate: "A highly efficient second-step concentration technique for bacteriophages and enteric viruses using ammonium sulfate and Tween 80" Armon et al., Can. J. Microbiol. 34:651, 1988 -Peter Muriana ********************************************************************* * Peter M. Muriana, Ph.D. Phone = (317)-494-8284 * * Dept. of Food Science FAX = (317)-494-7953 * * Purdue University E-mail = muriana@aclcb.purdue.edu * * W. Lafayette, IN 47907 * ********************************************************************* From owner-proteins@net.bio.net Wed Dec 01 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: sgex400@sghms.lon.ac.uk (MJ Duggan) Newsgroups: bionet.molbio.proteins Subject: Triton _X-114 Message-ID: <2d2pt0$cgp@mserv1.dl.ac.uk> Date: 25 Nov 93 17:26:56 GMT Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Lines: 20 Original-To: methods@dl.ac.uk (molbiol. methods newsgroup) Dear Netters, Has anybody out there used Triton-X-114 for the phase separation of membrane proteins? I am trying this following the method of Bordier (1981) J. Biol. Chem. _265_, 1604-1607. In this he ends up by spinning the T-X-114 phase down through a sucrose cushion. The problem that I have is that my T-X-114 phase floats above the buffer! (I am only washing the T-X-114 at present). The only difference that I can see between what I am doing and what is in the paper is that I am using PBS whereas he used Tris buffered saline (150 mM NaCl). Can anybody help. Am I doing anything wrong or is the paper wrong or misreadable? Any help would be welcome, I will post a summary if there is any interest. Thanks in advance, Michael Duggan From owner-proteins@net.bio.net Wed Dec 01 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!nih-csl!jowens.nci.nih.gov!jow From: jow@helix.nih.gov (Jim Owens) Newsgroups: bionet.molbio.proteins Subject: Keyhole Limpet hemocyanin Message-ID: <1993Dec2.151948.14121@alw.nih.gov> Date: 2 Dec 93 15:19:48 GMT Sender: postman@alw.nih.gov (AMDS Postmaster) Organization: NIH, Lab of Genetics Lines: 19 X-Xxmessage-Id: X-Xxdate: Thu, 2 Dec 93 15: 21:55 GMT X-Useragent: Version 1.1.3 I am looking for information about hemocyanin(s) of the Giant Keyhole Limpet. KLH (keyhole limpet hemocyanan) is a favorite carrier protein for haptens for immunologists, but there seems to be very little known about the structure in comparison to octopus or crab hemocyanins. That makes it hard to determine such things as number of haptens per molecule of KLH and how many haptens can be attached. I have not been able to find anyone who is actively studying this hemocyanin and have only found vague references to number of subunits and how hard they are to separate. There was an Italian group which gave some information in a Symposium volume about 5 or 6 years ago. If someone would be so kind as to point me in the direction of someone who knows about KLH or point me to references I would be eternally (well, for a week or two) grateful. Thanks in advance, Jim Owens From owner-proteins@net.bio.net Thu Dec 02 22:00:00 1993 Path: biosci!BCRSSU.AGR.CA!RAMPITSCH From: RAMPITSCH@BCRSSU.AGR.CA Newsgroups: bionet.molbio.proteins Subject: Prestained markers Message-ID: <01H622Y1WJLE000TU9@GW.AGR.CA> Date: 4 Dec 93 02:28:55 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 27 >I think I have seen a description of how to stain protein molecular >weight markers prior to electrophoresis somewere but can not remember >were I saw it. I think it was Coomassie that was used. >I know that there is a comersial source of something called pre-LMW/HMW. >The important thing is that I would like to be able to see the size >standard while running the gel, the gels I use is standard SDS-PAGE >adopted from Laemmli. >All replies appreciated. >Lars Snogerup >Plant biochemistry >U of Lund, Sweden BRL also makes these markers and as metioned (in another reply), they are not as accurate as unstained markers; they have another advantage though: they show up on N-C after western transfer which helps to align the blot with the gel. -------------------------------------------------------------------------------- Chris Rampitsch | RAMPITSCH@BCRSSU.AGR.CA Dept. Plant Science, Univ. of BC | Phone (604) 494-7711 Vancouver, British Columbia | Fax (604) 494-0755 Canada V6T 2A2 _/\_ ---------------------------------- __\ /__ ------------------------------------ "Sometimes I sit 'n' think... \__ __/ ...Sometimes I jes sit" ______________________________________||________________________________________ From owner-proteins@net.bio.net Thu Dec 02 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!EU.net!howland.reston.ans.net!spool.mu.edu!umn.edu!news.cs.indiana.edu!nstn.ns.ca!ac.dal.ca!arlin From: arlin@ac.dal.ca Newsgroups: bionet.molbio.proteins Subject: Re: help: want an advice Message-ID: <1993Nov30.084938.18544@ac.dal.ca> Date: 30 Nov 93 12:49:38 GMT References: <2ddrqk$1ov@pollux.usc.edu> Organization: Dalhousie University, Halifax, Nova Scotia, Canada Lines: 10 In article , robison1@husc10.harvard.edu (Keith Robison) writes: > An excellent book is "An Introduction to Protein Structure" by > Carl Branden and John Tooze. It is well-written (at a Scientific > American sort of level) and with nice color illustrations. > > Keith Robison I agree. This book is published by Garland (New York, 1991), ISBN 0-8153-0270-3 (paperback), 300 pp with lots of nice diagrams that were drawn specifically for the book. From owner-proteins@net.bio.net Thu Dec 02 22:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!embl-heidelberg.de!uni-heidelberg!rz.uni-karlsruhe.de!news.uni-ulm.de!news.belwue.de!news.dfn.de! zib-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!ipp-garching.mpg.de!alf.biochem.mpg.de!krasel From: krasel@alf.biochem.mpg.de (Cornelius Krasel) Newsgroups: bionet.molbio.proteins Subject: Re: Pre-staining of MW markers with Coomassie Message-ID: <2dnudbINNgvo@sat.ipp-garching.mpg.de> Date: 3 Dec 93 17:52:43 GMT References: <1993Dec3.133401.9480@nomina.lu.se> Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 20 NNTP-Posting-Host: alf.biochem.mpg.de X-Newsreader: TIN [version 1.1 PL8] RoundUp (Lars.S@Plantbio.lu.se) wrote: : I know that there is a comersial source of something called pre-LMW/HMW. : The important thing is that I would like to be able to see the size : standard while running the gel, the gels I use is standard SDS-PAGE : adopted from Laemmli. BioRad is one of several companies which sell prestained markers for SDS-PAGE. A certain disadvantage is that prestaining changes the MW of the protein slightly. Since staining is a semiquantitative :-) process, bands of prestained markers are usually broader than bands of unstained markers. I am not affiliated with BioRad, I just use their products. --Cornelius. -- /* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */ /* email: krasel@alf.biochem.mpg.de fax: +49 89 8578 3975 */ /* "People are DNA's way of making more DNA." (R. Dawkins/anonymous) */ From owner-proteins@net.bio.net Thu Dec 02 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!sunic!news.lth.se!news.lu.se!q700.plantbio.lu.se!Lars.S From: Lars.S@Plantbio.lu.se (RoundUp) Newsgroups: bionet.molbio.proteins Subject: Pre-staining of MW markers with Coomassie Message-ID: <1993Dec3.133401.9480@nomina.lu.se> Date: 3 Dec 93 13:34:01 GMT Sender: news@nomina.lu.se (USENET News System) Organization: Plant biochemistry U of Lund Lines: 13 X-Xxmessage-Id: X-Xxdate: Fri, 3 Dec 93 12:36:49 GMT Nntp-Posting-Host: q700.plantbio.lu.se X-Useragent: Nuntius v1.1.2 Hello, I think I have seen a description of how to stain protein molecular weight markers prior to electrophoresis somewere but can not remember were I saw it. I think it was Coomassie that was used. I know that there is a comersial source of something called pre-LMW/HMW. The important thing is that I would like to be able to see the size standard while running the gel, the gels I use is standard SDS-PAGE adopted from Laemmli. All replies appreciated. Lars Snogerup Plant biochemistry U of Lund, Sweden From owner-proteins@net.bio.net Thu Dec 02 22:00:00 1993 Path: biosci!lhc!darwin.sura.net!fconvx.ncifcrf.gov!fcs260c!mack From: mack@fcs260c.ncifcrf.gov (Joe Mack) Newsgroups: bionet.molbio.proteins Subject: Re: Pre-staining of MW markers with Coomassie Message-ID: Date: 3 Dec 93 20:39:47 GMT References: <1993Dec3.133401.9480@nomina.lu.se> Sender: usenet@ncifcrf.gov (C News) Organization: Frederick Cancer Research and Development Center Lines: 21 Nntp-Posting-Host: fcs260c.ncifcrf.gov In article <1993Dec3.133401.9480@nomina.lu.se> RoundUp writes: >Hello, >I think I have seen a description of how to stain protein molecular >weight markers prior to electrophoresis somewere but can not remember >were I saw it. I think it was Coomassie that was used. >I know that there is a comersial source of something called pre-LMW/HMW. >The important thing is that I would like to be able to see the size >standard while running the gel, the gels I use is standard SDS-PAGE >adopted from Laemmli. >All replies appreciated. > >Lars Snogerup >Plant biochemistry >U of Lund, Sweden Do you want to staqin with coomassie or do you just want to see your markers. If the latter,m, then the rainbow markers (hwere wool dyes are used to make the proteins visible ) will do fine. However the MW are no longer accurate (so I stopped using them). Joe mack@ncifcrf.gov From owner-proteins@net.bio.net Fri Dec 03 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!festival!leeds.ac.uk!news From: venkat@scs.leeds.ac.uk (N B Venkateswarlu) Newsgroups: bionet.molbio.proteins,sarada@biovax.leeds.ac.uk Subject: Help regrading ESR spectral subtraction Message-ID: <1993Dec4.100634.25753@gps.leeds.ac.uk> Date: 4 Dec 93 10:06:34 GMT Sender: nntp@gps.leeds.ac.uk Organization: The University of Leeds, School of Computer Studies Lines: 29 Xref: biosci bionet.molbio.proteins:1103 Originator: venkat@csgi31 Dear Netters, I am trying to use spectral subtraction (well establised) described in Jost et al. [197x] to get the derivative spectra in ESR analysis. S/W was developed by one my predecessors. I am facing serious troubles with this since last 2 months. That S/W is working for the sample data sets provided by that predecessor but not with any other one. I repeated experiments number of times. But no use. I request you to help me in the following way: 1. I know that WINEPR package is available somewhere and works under windows. Ofcourse it is expensive (it seems). So, please let me know any similar or the same package availability on main frame systems such Silicon Graphics or Sun's etc. such that I can rlogin and that S/W if it is not possible to copy. So, I request you to help by conveying the information regarding this. 2. I am following the method of Jost et al[ 1972, Computers in Biology and Medicine]. In which both Two component and single component spetras will be normalised to have same double integral area before subtraction. Then substracted signal will be scaled to have peak-valey height of some other reference spectrum. Is this procedure is correct. Do you know any other procedure to carry out the same. I would be very grateful for your reply. I am hanging on this problem since last August. Thank You Sarada From owner-proteins@net.bio.net Fri Dec 03 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!torn!nott!cunews!freenet.carleton.ca!Freenet.carleton.ca!ac562 From: ac562@Freenet.carleton.ca (Robert J. Forster) Newsgroups: bionet.molbio.proteins Subject: Post-doc Protein Design and Expression Message-ID: Date: 4 Dec 93 21:00:11 GMT Sender: news@freenet.carleton.ca Organization: The National Capital FreeNet, Ottawa, Ontario, Canada Lines: 37 AGRICULTURE CANADA CENTRE FOR FOOD AND ANIMAL RESEARCH OTTAWA, ONTARIO A position is available immediately at the Centre for Food and Animal Research of the Research Branch of Agriculture Canada, Central Experimental Farm, Ottawa, Ont., to study peptide design, isolation, and structure. The goal of the research program is to design peptides with specific amino acid compositions which are intracellularly stable when expressed in prokaryotic cells, and to construct genes and expression systems for these peptides which function in selected rumen bacterial strains. Techniques employed are microbiological and molecular genetic techniques including DNA synthesis, sequencing, and PCR, protein purification techniques including HPLC, FPLC, and affinity chromatography, and physical characterisation methods including UV and CD spectroscopy. The position is supported by a Biotechnology Fellowship paying $35,000 per year. Applicants should have a PhD in protein chemistry or a related discipline with a working knowledge of recombinant DNA techniques. To apply, contact Dr. M. Hefford, Centre for Food and Animal Research, K. W. Neatby Bldg., CEF, Ottawa, Ontario K1A 0C6. Phone (613) 993-6002. Fax (613) 943-2353. or email ag150rf@ncccot2.agr.ca -- Bob Forster P.O. Box 493 Osgoode, ON K0A 2W0 From owner-proteins@net.bio.net Fri Dec 03 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!cs.utexas.edu!swrinde!menudo.uh.edu!Rosie.UH.EDU!BCHS1B From: bchs1b@Rosie.UH.EDU (Michael Benedik) Newsgroups: bionet.molbio.proteins Subject: Re: Native MW of beta-Galactosidase (E. coli) Message-ID: <2drme2$dfg@menudo.uh.edu> Date: 5 Dec 93 04:01:06 GMT References: <01H5XN9EPT4Y000RSG@nic.the.net> Reply-To: bchs1b@Rosie.UH.EDU Distribution: bionet Organization: University of Houston Lines: 19 NNTP-Posting-Host: rosie.uh.edu In article <01H5XN9EPT4Y000RSG@nic.the.net>, SHAUN%JASON.DECNET@relay.the.net ("Shaun D. Black") writes: >Does anyone have the native (tetrameric) molecular weight of E. coli beta- >galactosidase handy? Thanks in advance! Cheers, Shaun > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = > = Dept. of Biochemistry | University of Texas Health Center, at Tyler = > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Predicted molecular weight of monomer is 116,000, so for tetramer should be 464,000. This at least is what the computer says, I personally have not run a well calibrated sizing column to confirm. ---------------------------------------------------------------------- Michael Benedik INTERNET: Benedik@uh.edu Dept. of Biochemical & Biophysical Sciences University of Houston BITNET: Benedik@uhou ----------------------------------------------------------------------- From owner-proteins@net.bio.net Fri Dec 03 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!europa.eng.gtefsd.com!gatech!news-feed-1.peachnet.edu!umn.edu!lynx.unm.edu!dns1.NMSU.Edu!smori From: smori@nmsu.edu (Shahram Mori) Newsgroups: bionet.molbio.proteins Subject: ptn question? Message-ID: <2drcgiINN70b@dns1.NMSU.Edu> Date: 5 Dec 93 01:11:46 GMT Organization: New Mexico State University, Las Cruces, NM Lines: 6 NNTP-Posting-Host: dante.nmsu.edu X-Newsreader: TIN [version 1.2 PL1] Dear netters, What is the best way to store a stock of crude/ammonium sulfate ppted proteins. -4C, -20C or -70C Thanks for the help. Shahram From owner-proteins@net.bio.net Sat Dec 04 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!zaphod.crihan.fr!news.univ-rennes1.fr!cict.fr!ecstasy!maveyrau From: maveyrau@ecstasy.NoSubdomain.NoDomain (Laurent Maveyraud) Newsgroups: bionet.molbio.proteins Subject: Re: looking for proteins sequences Message-ID: <2dsrc0$j26@reseau.cict.fr> Date: 5 Dec 93 14:31:28 GMT Sender: maveyrau@ecstasy (Laurent Maveyraud) Organization: Laboratoire de Pharmacologie et Toxicologie Fondamentales (LPTF/CNRS, Toulouse) Lines: 29 NNTP-Posting-Host: 192.93.13.7 >Hi Netters, > >I have got a protein sequence and I would like to compare it with other >ones. Somebody there could tell me some information about how is the >easiest manner to proceed a roughly search? (database, software, time >required, etc). One of the numerous way is to use the UWGCG package, with the database Genembl. The option is TFASTA. This goes through the whole DNA database, translates all the sequences available in the six possible reading frames, and compares the results to your protein sequence (but I don't remember which algorithm/matrice are used). This search needs around 20min on a DEC3000-240 workstation. Software : UWGCG (University of Wisconsin Genetic Computer Group) it is available nearly everywhere there are molecular biology labs (option TFASTA) Database : Genembl, which is also from UWGCG, and is updated every 15 days (I think...) Time : well, this depends mainly on the machine you are using. It can range from 1hour to 15 min. I hope this helps Laurent Maveyraud Groupe de Cristallographie Biologique CEMES BP 4347 31055 Toulouse (France) maveyrau@cemes.fr From owner-proteins@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!news.cs.umb.edu!hsdndev!yale!yale.edu!nigel.msen.com!usenet.ins.cwru.edu!howland.reston.ans.net!pipex!sunic!isgate!news.rhi.hi.is!zjons From: zjons@rhi.hi.is (Zophonias Oddur Jonsson) Newsgroups: bionet.molbio.proteins,sci.chem Subject: Q: PO3-bond free energies in NAD+ Keywords: NAD+ NMN ATP Ligase Message-ID: <2dtia9$5vo@eldborg.rhi.hi.is> Date: 5 Dec 93 21:03:05 GMT Followup-To: bionet.molbio.proteins Organization: University of Iceland Lines: 32 Xref: biosci bionet.molbio.proteins:1116 sci.chem:9420 NNTP-Posting-Host: hengill.rhi.hi.is Hi all you experts! I have a question that I haven't been able to figure out by myself or with the help of my organic chemist friends, so I'll take the liberty to ask you all. Where or how can I find the free energies of the following bonds: The PO3-O-PO3 bonds between the nucleotides in NAD+, the Phosphor amide bond between epsilon-NH2 of Lysine and the PO3 of AMP and the PO3-O-PO3 bonds between, say two 5' linked Adenosyl nucleotides. ??? The reason I ask is that I want to get some Idea of the thermodynamics of the reaction that bacterial DNA ligases catalyse. They use NAD+ as their source of energy in a rather unusual reaction. They break it up and transfer the AMP part of it to a Lysine residue and then, in another step, transfer it from the lysine to the 5' end of the DNA strand being ligated. (The last step is then a plain nucleophilic attack by 3'-OH on the other side of the nick). I would expect that all these bonds have free energies somewhere close to 33 kj/mol, and that the energies of all the PO3-O-PO3 bonds are very similar, but then I'm no chemist, so what do I know? The question is, does anyone have better estimates? Do you think the reaction is exothermic or that it's the concentration of NAD+ that forces it to happen? Thank you for reading this Zophonias O. Jonsson Laboratory of Molecular Genetics University of Iceland zjons@rhi.hi.is _________________________________ if you think this is a silly question please flame me by e-mail. From owner-proteins@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!news.cs.umb.edu!hsdndev!yale!yale.edu!spool.mu.edu!darwin.sura.net!lhc!borduas!francis From: francis@borduas.nlm.nih.gov (Francis Ouellette) Newsgroups: bionet.molbio.proteins Subject: Re: looking for proteins sequences Message-ID: <1993Dec5.151819.9686@nlm.nih.gov> Date: 5 Dec 93 15:18:19 GMT References: Sender: news@nlm.nih.gov Distribution: bionet Organization: National Library of Medicine Lines: 43 X-Newsreader: Tin 1.1 PL4 mcpalmie@FOX.CCE.USP.BR (Mauricio Cesar Palmieri) writes: : I have got a protein sequence and I would like to compare it with other : ones. Somebody there could tell me some information about how is the : easiest manner to proceed a roughly search? (database, software, time : required, etc). One (of many!) easy way to do it is to use the BLAST Email server at NCBI: blast@ncbi.nlm.nih.gov There are many databases you can querry there, and the best is to get the information document, which you can get by mailing to the server with the word 'help' in the body of the text (blank subject line). if you need help from a person (not a mail server), you can Email this address: info@ncbi.nlm.nih.gov : database Most of the major protein and nucleic acid databases are there. : software You need is an Email account. : time Depends on your Internet connection and the size of the querry, and how many other people are using the server at the same time you are. The search itself can take from a few seconds to a few minutes. regards, francis -- | B.F. Francis Ouellette | | francis@ncbi.nlm.nih.gov From owner-proteins@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!news.cs.umb.edu!hsdndev!yale!yale.edu!spool.mu.edu!howland.reston.ans.net!pipex!zaphod.crihan.fr!news.univ-rennes1.fr!cict.fr!ecstasy!maveyrau From: maveyrau@ecstasy.NoSubdomain.NoDomain (Laurent Maveyraud) Newsgroups: bionet.molbio.proteins Subject: Re: looking for proteins sequences Message-ID: <2dsrc0$j26@reseau.cict.fr> Date: 5 Dec 93 14:31:28 GMT Sender: maveyrau@ecstasy (Laurent Maveyraud) Organization: Laboratoire de Pharmacologie et Toxicologie Fondamentales (LPTF/CNRS, Toulouse) Lines: 29 NNTP-Posting-Host: 192.93.13.7 >Hi Netters, > >I have got a protein sequence and I would like to compare it with other >ones. Somebody there could tell me some information about how is the >easiest manner to proceed a roughly search? (database, software, time >required, etc). One of the numerous way is to use the UWGCG package, with the database Genembl. The option is TFASTA. This goes through the whole DNA database, translates all the sequences available in the six possible reading frames, and compares the results to your protein sequence (but I don't remember which algorithm/matrice are used). This search needs around 20min on a DEC3000-240 workstation. Software : UWGCG (University of Wisconsin Genetic Computer Group) it is available nearly everywhere there are molecular biology labs (option TFASTA) Database : Genembl, which is also from UWGCG, and is updated every 15 days (I think...) Time : well, this depends mainly on the machine you are using. It can range from 1hour to 15 min. I hope this helps Laurent Maveyraud Groupe de Cristallographie Biologique CEMES BP 4347 31055 Toulouse (France) maveyrau@cemes.fr From owner-proteins@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!sunic!isgate!news.rhi.hi.is!zjons From: zjons@rhi.hi.is (Zophonias Oddur Jonsson) Newsgroups: bionet.molbio.proteins,sci.chem Subject: Q: PO3-bond free energies in NAD+ Keywords: NAD+ NMN ATP Ligase Message-ID: <2dtia9$5vo@eldborg.rhi.hi.is> Date: 5 Dec 93 21:03:05 GMT Followup-To: bionet.molbio.proteins Organization: University of Iceland Lines: 32 Xref: biosci bionet.molbio.proteins:1110 sci.chem:9418 NNTP-Posting-Host: hengill.rhi.hi.is Hi all you experts! I have a question that I haven't been able to figure out by myself or with the help of my organic chemist friends, so I'll take the liberty to ask you all. Where or how can I find the free energies of the following bonds: The PO3-O-PO3 bonds between the nucleotides in NAD+, the Phosphor amide bond between epsilon-NH2 of Lysine and the PO3 of AMP and the PO3-O-PO3 bonds between, say two 5' linked Adenosyl nucleotides. ??? The reason I ask is that I want to get some Idea of the thermodynamics of the reaction that bacterial DNA ligases catalyse. They use NAD+ as their source of energy in a rather unusual reaction. They break it up and transfer the AMP part of it to a Lysine residue and then, in another step, transfer it from the lysine to the 5' end of the DNA strand being ligated. (The last step is then a plain nucleophilic attack by 3'-OH on the other side of the nick). I would expect that all these bonds have free energies somewhere close to 33 kj/mol, and that the energies of all the PO3-O-PO3 bonds are very similar, but then I'm no chemist, so what do I know? The question is, does anyone have better estimates? Do you think the reaction is exothermic or that it's the concentration of NAD+ that forces it to happen? Thank you for reading this Zophonias O. Jonsson Laboratory of Molecular Genetics University of Iceland zjons@rhi.hi.is _________________________________ if you think this is a silly question please flame me by e-mail. From owner-proteins@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!darwin.sura.net!lhc!borduas!francis From: francis@borduas.nlm.nih.gov (Francis Ouellette) Newsgroups: bionet.molbio.proteins Subject: Re: looking for proteins sequences Message-ID: <1993Dec5.151819.9686@nlm.nih.gov> Date: 5 Dec 93 15:18:19 GMT References: Sender: news@nlm.nih.gov Distribution: bionet Organization: National Library of Medicine Lines: 43 X-Newsreader: Tin 1.1 PL4 mcpalmie@FOX.CCE.USP.BR (Mauricio Cesar Palmieri) writes: : I have got a protein sequence and I would like to compare it with other : ones. Somebody there could tell me some information about how is the : easiest manner to proceed a roughly search? (database, software, time : required, etc). One (of many!) easy way to do it is to use the BLAST Email server at NCBI: blast@ncbi.nlm.nih.gov There are many databases you can querry there, and the best is to get the information document, which you can get by mailing to the server with the word 'help' in the body of the text (blank subject line). if you need help from a person (not a mail server), you can Email this address: info@ncbi.nlm.nih.gov : database Most of the major protein and nucleic acid databases are there. : software You need is an Email account. : time Depends on your Internet connection and the size of the querry, and how many other people are using the server at the same time you are. The search itself can take from a few seconds to a few minutes. regards, francis -- | B.F. Francis Ouellette | | francis@ncbi.nlm.nih.gov From owner-proteins@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!CS.Arizona.EDU!noao!asuvax!cs.utexas.edu!howland.reston.ans.net!pipex!sunic!isgate!news.rhi.hi.is!zjons From: zjons@rhi.hi.is (Zophonias Oddur Jonsson) Newsgroups: bionet.molbio.proteins,sci.chem Subject: Q: PO3-bond free energies in NAD+ Keywords: NAD+ NMN ATP Ligase Message-ID: <2dtia9$5vo@eldborg.rhi.hi.is> Date: 5 Dec 93 21:03:05 GMT Followup-To: bionet.molbio.proteins Organization: University of Iceland Lines: 32 Xref: biosci bionet.molbio.proteins:1108 sci.chem:9417 NNTP-Posting-Host: hengill.rhi.hi.is Hi all you experts! I have a question that I haven't been able to figure out by myself or with the help of my organic chemist friends, so I'll take the liberty to ask you all. Where or how can I find the free energies of the following bonds: The PO3-O-PO3 bonds between the nucleotides in NAD+, the Phosphor amide bond between epsilon-NH2 of Lysine and the PO3 of AMP and the PO3-O-PO3 bonds between, say two 5' linked Adenosyl nucleotides. ??? The reason I ask is that I want to get some Idea of the thermodynamics of the reaction that bacterial DNA ligases catalyse. They use NAD+ as their source of energy in a rather unusual reaction. They break it up and transfer the AMP part of it to a Lysine residue and then, in another step, transfer it from the lysine to the 5' end of the DNA strand being ligated. (The last step is then a plain nucleophilic attack by 3'-OH on the other side of the nick). I would expect that all these bonds have free energies somewhere close to 33 kj/mol, and that the energies of all the PO3-O-PO3 bonds are very similar, but then I'm no chemist, so what do I know? The question is, does anyone have better estimates? Do you think the reaction is exothermic or that it's the concentration of NAD+ that forces it to happen? Thank you for reading this Zophonias O. Jonsson Laboratory of Molecular Genetics University of Iceland zjons@rhi.hi.is _________________________________ if you think this is a silly question please flame me by e-mail. From owner-proteins@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!news.cs.umb.edu!hsdndev!yale!yale.edu!spool.mu.edu!howland.reston.ans.net!cs.utexas.edu!swrinde!menudo.uh.edu!Rosie.UH.EDU!BCHS1B From: bchs1b@Rosie.UH.EDU (Michael Benedik) Newsgroups: bionet.molbio.proteins Subject: Re: Native MW of beta-Galactosidase (E. coli) Message-ID: <2drme2$dfg@menudo.uh.edu> Date: 5 Dec 93 04:01:06 GMT References: <01H5XN9EPT4Y000RSG@nic.the.net> Reply-To: bchs1b@Rosie.UH.EDU Distribution: bionet Organization: University of Houston Lines: 19 NNTP-Posting-Host: rosie.uh.edu In article <01H5XN9EPT4Y000RSG@nic.the.net>, SHAUN%JASON.DECNET@relay.the.net ("Shaun D. Black") writes: >Does anyone have the native (tetrameric) molecular weight of E. coli beta- >galactosidase handy? Thanks in advance! Cheers, Shaun > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = > = Dept. of Biochemistry | University of Texas Health Center, at Tyler = > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Predicted molecular weight of monomer is 116,000, so for tetramer should be 464,000. This at least is what the computer says, I personally have not run a well calibrated sizing column to confirm. ---------------------------------------------------------------------- Michael Benedik INTERNET: Benedik@uh.edu Dept. of Biochemical & Biophysical Sciences University of Houston BITNET: Benedik@uhou ----------------------------------------------------------------------- From owner-proteins@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.molbio.proteins,bionet.software Subject: Re: looking for proteins sequences Message-ID: <1993Dec6.074754.23544@comp.bioz.unibas.ch> Date: 6 Dec 93 07:47:54 GMT References: <2dsrc0$j26@reseau.cict.fr> Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Reply-To: doelz@urz.unibas.ch Organization: EMBnet Switzerland [BASEL] Lines: 138 Xref: biosci bionet.molbio.proteins:1112 bionet.software:6655 Nntp-Posting-Host: biox.embnet.unibas.ch In article <2dsrc0$j26@reseau.cict.fr>, maveyrau@ecstasy.NoSubdomain.NoDomain (Laurent Maveyraud) writes: |> Query from mcpalmie@FOX.CCE.USP.BR (Mauricio Cesar Palmieri): |> ... |> >ones. Somebody there could tell me some information about how is the |> >easiest manner to proceed a roughly search? (database, software, time |> >required, etc). The software you may choose balances speed vs. sensitivity, and it very much depends on the question you ask. There are three options (1) Rely on the network (2) rely on your site (3) Do everything yourself Option three, obviously, is time consuming and usually does not pay off. You should not need to install software and databases yourself if you work in a larger environment because central services are cost- effective and therefore provided usually. If you do not enjoy such comfort but need to initiate one the best were to visit a site where it's already running (better even, two or three different sites running different environments). Option one, the network, may turn out to be a Damokles sword; as you get what you paid for. Most of the services are "free". Many of the services provided on the net are spawned from research activities and therefore continuously suffer from funding, thus, are continuously in danger to degrade, or cease to exist. There are a few exceptions, thogh, like the services of the EMBL data library or the national services from EMBnet in Europe, and the NCBI in the US. The available services on the network have been collected by Amos Bairoch and are available on various servers, on our mirror server you will find the data on nic.switch.ch as mirror/embnet-ch/other-data/info/serv_ema.txt.Z With respect to option two, the central services, you might want to consider querying your national Center in Brasil. Goran (adresses below) will provide you answers to your questions if you would like to get either services there or an advice. Any EMBnet node has an entry in 'The Nodes of EMBnet' database which is available as Postscript format on nic.switch.ch in mirror/embnet-ch/info/embnet The embnet.dat file is a plain ASCII file and there are nice postscript versions with additional information as well. There is a Brasilian node in Brasilea which serves the community according to as imilar structure as the EMBnet nodes do in Europe, the Brazilian Molecular Biology and Biotechnology Network (BMBBNet). For more information, ask at ------------------------------------------------------------------------ | Goran Neshich | | | CENARGEN/EMBRAPA | e-mail: neshich@cenargen.embrapa.br | | S.A.I.N. Parque Rural, Final W5 | | | Asa Norte | Phone: +55 (61)273-0100 ext 127 | | 70770-900, Brasilia-D.F.-BRASIL | Fax: +55 (61)274-3212 | ------------------------------------------------------------------------ |> |> |> One of the numerous way is to use the UWGCG package, with the database |> Genembl. The option is TFASTA. This goes through the whole DNA database, TFASTA belongs to the FASTA package written by William R. Pearson originally described in Science (Lipman and Pearson, (1985) Science 227:1435-1441). The Genetics Computer Group, Inc. (Madison, Wisconsin) distributes a version which is adapted to their package. ... |> Software : UWGCG (University of Wisconsin Genetic Computer Group) it is |> available nearly everywhere there are molecular biology labs The package in question arose from an academic group (UWGCG) but is now comercially managed (Info at beers@gcg.com). Due to its history and economical factors, it is installed at a large basis. We have enjoyed excellent results arising from running this package since 1987. However, it is important to emphasize that other packages are available, such as the Intelligenetics Software Packahe (known as IG Suite, Info at ig-consultant@presto.ig.com), and others. There are many packages available from the public domain, though, these usually cover only a special (but very extensively covered) set of a particular activity, e.g. sequence searching, e.g., he FASTA was mentioned above, and the NCBI has released the 'BLAST' suite of programs. |> |> Database : Genembl, which is also from UWGCG, and is updated every 15 days (I think...) 'Genembl' is a term for a merged database used in the GCG package. On the basis of accession numbers, Genbank and EMBL are excluded in the corresponding database; e.g., in the US you would normally run GENBANK with a EMBL exclusion set, and in Europe you will have a EMBL with a Genbank exclusion set. The update frequency is a matter of your administrator, we do EMBL daily and GENBANK weekly, most sites in Switzerland maintain a weekly GCG GENEMBL data update. There oare other merged collections out there, PATCHX, OWL, and others. |> |> Time : well, this depends mainly on the machine you are using. It can range from 1hour to 15 min. BLAST (software from the NCBI) takes only a few seconds if peptide runs vs. peptice straight, and a Smith and Waterman search on a massively parallel machine (software from the Edinburgh team) doen't take longer either. The latter run on a deskside, 4 year old hardware might easily take 5 hours CPU to complete. The search software available ranges from scans of identity to sophisticated methods of fragment pattern searching, and from browsing the database with quick-but-dirty to extensive homology evaluations searching with profiles. ISEARCH (PIR), (T)FASTA (Pearson), BLAST (NCBI), WORDSEARCH(UWGCG), TWORDSEARCH(Rice), BLAZE (Intelligenetics), MPsearch(Collins et al, also as BLITZ), PROFILE methods (GRIBSKOV), FLASH (IBM), and many, many other programs have a wide area of application. So the range depends on * algorithm used * hardware used * question asked * (occasionally) length of the sequence Regards Reinhard -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ftp mirror at nic.switch.ch ----------------------------------------- From owner-proteins@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!cs.utexas.edu!howland.reston.ans.net!xlink.net!scsing.switch.ch!urz.unibas.ch!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.molbio.proteins,bionet.software Subject: Re: looking for proteins sequences Message-ID: <1993Dec6.074754.23544@comp.bioz.unibas.ch> Date: 6 Dec 93 07:47:54 GMT References: <2dsrc0$j26@reseau.cict.fr> Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Reply-To: doelz@urz.unibas.ch Organization: EMBnet Switzerland [BASEL] Lines: 138 Xref: biosci bionet.molbio.proteins:1111 bionet.software:6654 Nntp-Posting-Host: biox.embnet.unibas.ch In article <2dsrc0$j26@reseau.cict.fr>, maveyrau@ecstasy.NoSubdomain.NoDomain (Laurent Maveyraud) writes: |> Query from mcpalmie@FOX.CCE.USP.BR (Mauricio Cesar Palmieri): |> ... |> >ones. Somebody there could tell me some information about how is the |> >easiest manner to proceed a roughly search? (database, software, time |> >required, etc). The software you may choose balances speed vs. sensitivity, and it very much depends on the question you ask. There are three options (1) Rely on the network (2) rely on your site (3) Do everything yourself Option three, obviously, is time consuming and usually does not pay off. You should not need to install software and databases yourself if you work in a larger environment because central services are cost- effective and therefore provided usually. If you do not enjoy such comfort but need to initiate one the best were to visit a site where it's already running (better even, two or three different sites running different environments). Option one, the network, may turn out to be a Damokles sword; as you get what you paid for. Most of the services are "free". Many of the services provided on the net are spawned from research activities and therefore continuously suffer from funding, thus, are continuously in danger to degrade, or cease to exist. There are a few exceptions, thogh, like the services of the EMBL data library or the national services from EMBnet in Europe, and the NCBI in the US. The available services on the network have been collected by Amos Bairoch and are available on various servers, on our mirror server you will find the data on nic.switch.ch as mirror/embnet-ch/other-data/info/serv_ema.txt.Z With respect to option two, the central services, you might want to consider querying your national Center in Brasil. Goran (adresses below) will provide you answers to your questions if you would like to get either services there or an advice. Any EMBnet node has an entry in 'The Nodes of EMBnet' database which is available as Postscript format on nic.switch.ch in mirror/embnet-ch/info/embnet The embnet.dat file is a plain ASCII file and there are nice postscript versions with additional information as well. There is a Brasilian node in Brasilea which serves the community according to as imilar structure as the EMBnet nodes do in Europe, the Brazilian Molecular Biology and Biotechnology Network (BMBBNet). For more information, ask at ------------------------------------------------------------------------ | Goran Neshich | | | CENARGEN/EMBRAPA | e-mail: neshich@cenargen.embrapa.br | | S.A.I.N. Parque Rural, Final W5 | | | Asa Norte | Phone: +55 (61)273-0100 ext 127 | | 70770-900, Brasilia-D.F.-BRASIL | Fax: +55 (61)274-3212 | ------------------------------------------------------------------------ |> |> |> One of the numerous way is to use the UWGCG package, with the database |> Genembl. The option is TFASTA. This goes through the whole DNA database, TFASTA belongs to the FASTA package written by William R. Pearson originally described in Science (Lipman and Pearson, (1985) Science 227:1435-1441). The Genetics Computer Group, Inc. (Madison, Wisconsin) distributes a version which is adapted to their package. ... |> Software : UWGCG (University of Wisconsin Genetic Computer Group) it is |> available nearly everywhere there are molecular biology labs The package in question arose from an academic group (UWGCG) but is now comercially managed (Info at beers@gcg.com). Due to its history and economical factors, it is installed at a large basis. We have enjoyed excellent results arising from running this package since 1987. However, it is important to emphasize that other packages are available, such as the Intelligenetics Software Packahe (known as IG Suite, Info at ig-consultant@presto.ig.com), and others. There are many packages available from the public domain, though, these usually cover only a special (but very extensively covered) set of a particular activity, e.g. sequence searching, e.g., he FASTA was mentioned above, and the NCBI has released the 'BLAST' suite of programs. |> |> Database : Genembl, which is also from UWGCG, and is updated every 15 days (I think...) 'Genembl' is a term for a merged database used in the GCG package. On the basis of accession numbers, Genbank and EMBL are excluded in the corresponding database; e.g., in the US you would normally run GENBANK with a EMBL exclusion set, and in Europe you will have a EMBL with a Genbank exclusion set. The update frequency is a matter of your administrator, we do EMBL daily and GENBANK weekly, most sites in Switzerland maintain a weekly GCG GENEMBL data update. There oare other merged collections out there, PATCHX, OWL, and others. |> |> Time : well, this depends mainly on the machine you are using. It can range from 1hour to 15 min. BLAST (software from the NCBI) takes only a few seconds if peptide runs vs. peptice straight, and a Smith and Waterman search on a massively parallel machine (software from the Edinburgh team) doen't take longer either. The latter run on a deskside, 4 year old hardware might easily take 5 hours CPU to complete. The search software available ranges from scans of identity to sophisticated methods of fragment pattern searching, and from browsing the database with quick-but-dirty to extensive homology evaluations searching with profiles. ISEARCH (PIR), (T)FASTA (Pearson), BLAST (NCBI), WORDSEARCH(UWGCG), TWORDSEARCH(Rice), BLAZE (Intelligenetics), MPsearch(Collins et al, also as BLITZ), PROFILE methods (GRIBSKOV), FLASH (IBM), and many, many other programs have a wide area of application. So the range depends on * algorithm used * hardware used * question asked * (occasionally) length of the sequence Regards Reinhard -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ftp mirror at nic.switch.ch ----------------------------------------- From owner-proteins@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!news.cs.umb.edu!hsdndev!yale!yale.edu!newsserver.jvnc.net!howland.reston.ans.net!xlink.net!scsing.switch.ch!urz.unibas.ch!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.molbio.proteins,bionet.software Subject: Re: looking for proteins sequences Message-ID: <1993Dec6.074754.23544@comp.bioz.unibas.ch> Date: 6 Dec 93 07:47:54 GMT References: <2dsrc0$j26@reseau.cict.fr> Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Reply-To: doelz@urz.unibas.ch Organization: EMBnet Switzerland [BASEL] Lines: 138 Xref: biosci bionet.molbio.proteins:1117 bionet.software:6667 Nntp-Posting-Host: biox.embnet.unibas.ch In article <2dsrc0$j26@reseau.cict.fr>, maveyrau@ecstasy.NoSubdomain.NoDomain (Laurent Maveyraud) writes: |> Query from mcpalmie@FOX.CCE.USP.BR (Mauricio Cesar Palmieri): |> ... |> >ones. Somebody there could tell me some information about how is the |> >easiest manner to proceed a roughly search? (database, software, time |> >required, etc). The software you may choose balances speed vs. sensitivity, and it very much depends on the question you ask. There are three options (1) Rely on the network (2) rely on your site (3) Do everything yourself Option three, obviously, is time consuming and usually does not pay off. You should not need to install software and databases yourself if you work in a larger environment because central services are cost- effective and therefore provided usually. If you do not enjoy such comfort but need to initiate one the best were to visit a site where it's already running (better even, two or three different sites running different environments). Option one, the network, may turn out to be a Damokles sword; as you get what you paid for. Most of the services are "free". Many of the services provided on the net are spawned from research activities and therefore continuously suffer from funding, thus, are continuously in danger to degrade, or cease to exist. There are a few exceptions, thogh, like the services of the EMBL data library or the national services from EMBnet in Europe, and the NCBI in the US. The available services on the network have been collected by Amos Bairoch and are available on various servers, on our mirror server you will find the data on nic.switch.ch as mirror/embnet-ch/other-data/info/serv_ema.txt.Z With respect to option two, the central services, you might want to consider querying your national Center in Brasil. Goran (adresses below) will provide you answers to your questions if you would like to get either services there or an advice. Any EMBnet node has an entry in 'The Nodes of EMBnet' database which is available as Postscript format on nic.switch.ch in mirror/embnet-ch/info/embnet The embnet.dat file is a plain ASCII file and there are nice postscript versions with additional information as well. There is a Brasilian node in Brasilea which serves the community according to as imilar structure as the EMBnet nodes do in Europe, the Brazilian Molecular Biology and Biotechnology Network (BMBBNet). For more information, ask at ------------------------------------------------------------------------ | Goran Neshich | | | CENARGEN/EMBRAPA | e-mail: neshich@cenargen.embrapa.br | | S.A.I.N. Parque Rural, Final W5 | | | Asa Norte | Phone: +55 (61)273-0100 ext 127 | | 70770-900, Brasilia-D.F.-BRASIL | Fax: +55 (61)274-3212 | ------------------------------------------------------------------------ |> |> |> One of the numerous way is to use the UWGCG package, with the database |> Genembl. The option is TFASTA. This goes through the whole DNA database, TFASTA belongs to the FASTA package written by William R. Pearson originally described in Science (Lipman and Pearson, (1985) Science 227:1435-1441). The Genetics Computer Group, Inc. (Madison, Wisconsin) distributes a version which is adapted to their package. ... |> Software : UWGCG (University of Wisconsin Genetic Computer Group) it is |> available nearly everywhere there are molecular biology labs The package in question arose from an academic group (UWGCG) but is now comercially managed (Info at beers@gcg.com). Due to its history and economical factors, it is installed at a large basis. We have enjoyed excellent results arising from running this package since 1987. However, it is important to emphasize that other packages are available, such as the Intelligenetics Software Packahe (known as IG Suite, Info at ig-consultant@presto.ig.com), and others. There are many packages available from the public domain, though, these usually cover only a special (but very extensively covered) set of a particular activity, e.g. sequence searching, e.g., he FASTA was mentioned above, and the NCBI has released the 'BLAST' suite of programs. |> |> Database : Genembl, which is also from UWGCG, and is updated every 15 days (I think...) 'Genembl' is a term for a merged database used in the GCG package. On the basis of accession numbers, Genbank and EMBL are excluded in the corresponding database; e.g., in the US you would normally run GENBANK with a EMBL exclusion set, and in Europe you will have a EMBL with a Genbank exclusion set. The update frequency is a matter of your administrator, we do EMBL daily and GENBANK weekly, most sites in Switzerland maintain a weekly GCG GENEMBL data update. There oare other merged collections out there, PATCHX, OWL, and others. |> |> Time : well, this depends mainly on the machine you are using. It can range from 1hour to 15 min. BLAST (software from the NCBI) takes only a few seconds if peptide runs vs. peptice straight, and a Smith and Waterman search on a massively parallel machine (software from the Edinburgh team) doen't take longer either. The latter run on a deskside, 4 year old hardware might easily take 5 hours CPU to complete. The search software available ranges from scans of identity to sophisticated methods of fragment pattern searching, and from browsing the database with quick-but-dirty to extensive homology evaluations searching with profiles. ISEARCH (PIR), (T)FASTA (Pearson), BLAST (NCBI), WORDSEARCH(UWGCG), TWORDSEARCH(Rice), BLAZE (Intelligenetics), MPsearch(Collins et al, also as BLITZ), PROFILE methods (GRIBSKOV), FLASH (IBM), and many, many other programs have a wide area of application. So the range depends on * algorithm used * hardware used * question asked * (occasionally) length of the sequence Regards Reinhard -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ftp mirror at nic.switch.ch ----------------------------------------- From owner-proteins@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!lhc!darwin.sura.net!howland.reston.ans.net!pipex!sunic!isgate!news.rhi.hi.is!zjons From: zjons@rhi.hi.is (Zophonias Oddur Jonsson) Newsgroups: bionet.molbio.proteins,sci.chem Subject: Q: PO3-bond free energies in NAD+ Keywords: NAD+ NMN ATP Ligase Message-ID: <2dtia9$5vo@eldborg.rhi.hi.is> Date: 5 Dec 93 21:03:05 GMT Followup-To: bionet.molbio.proteins Organization: University of Iceland Lines: 32 Xref: biosci bionet.molbio.proteins:1120 sci.chem:9421 NNTP-Posting-Host: hengill.rhi.hi.is Hi all you experts! I have a question that I haven't been able to figure out by myself or with the help of my organic chemist friends, so I'll take the liberty to ask you all. Where or how can I find the free energies of the following bonds: The PO3-O-PO3 bonds between the nucleotides in NAD+, the Phosphor amide bond between epsilon-NH2 of Lysine and the PO3 of AMP and the PO3-O-PO3 bonds between, say two 5' linked Adenosyl nucleotides. ??? The reason I ask is that I want to get some Idea of the thermodynamics of the reaction that bacterial DNA ligases catalyse. They use NAD+ as their source of energy in a rather unusual reaction. They break it up and transfer the AMP part of it to a Lysine residue and then, in another step, transfer it from the lysine to the 5' end of the DNA strand being ligated. (The last step is then a plain nucleophilic attack by 3'-OH on the other side of the nick). I would expect that all these bonds have free energies somewhere close to 33 kj/mol, and that the energies of all the PO3-O-PO3 bonds are very similar, but then I'm no chemist, so what do I know? The question is, does anyone have better estimates? Do you think the reaction is exothermic or that it's the concentration of NAD+ that forces it to happen? Thank you for reading this Zophonias O. Jonsson Laboratory of Molecular Genetics University of Iceland zjons@rhi.hi.is _________________________________ if you think this is a silly question please flame me by e-mail. From owner-proteins@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!lhc!darwin.sura.net!howland.reston.ans.net!xlink.net!scsing.switch.ch!urz.unibas.ch!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.molbio.proteins,bionet.software Subject: Re: looking for proteins sequences Message-ID: <1993Dec6.074754.23544@comp.bioz.unibas.ch> Date: 6 Dec 93 07:47:54 GMT References: <2dsrc0$j26@reseau.cict.fr> Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Reply-To: doelz@urz.unibas.ch Organization: EMBnet Switzerland [BASEL] Lines: 138 Xref: biosci bionet.molbio.proteins:1119 bionet.software:6676 Nntp-Posting-Host: biox.embnet.unibas.ch In article <2dsrc0$j26@reseau.cict.fr>, maveyrau@ecstasy.NoSubdomain.NoDomain (Laurent Maveyraud) writes: |> Query from mcpalmie@FOX.CCE.USP.BR (Mauricio Cesar Palmieri): |> ... |> >ones. Somebody there could tell me some information about how is the |> >easiest manner to proceed a roughly search? (database, software, time |> >required, etc). The software you may choose balances speed vs. sensitivity, and it very much depends on the question you ask. There are three options (1) Rely on the network (2) rely on your site (3) Do everything yourself Option three, obviously, is time consuming and usually does not pay off. You should not need to install software and databases yourself if you work in a larger environment because central services are cost- effective and therefore provided usually. If you do not enjoy such comfort but need to initiate one the best were to visit a site where it's already running (better even, two or three different sites running different environments). Option one, the network, may turn out to be a Damokles sword; as you get what you paid for. Most of the services are "free". Many of the services provided on the net are spawned from research activities and therefore continuously suffer from funding, thus, are continuously in danger to degrade, or cease to exist. There are a few exceptions, thogh, like the services of the EMBL data library or the national services from EMBnet in Europe, and the NCBI in the US. The available services on the network have been collected by Amos Bairoch and are available on various servers, on our mirror server you will find the data on nic.switch.ch as mirror/embnet-ch/other-data/info/serv_ema.txt.Z With respect to option two, the central services, you might want to consider querying your national Center in Brasil. Goran (adresses below) will provide you answers to your questions if you would like to get either services there or an advice. Any EMBnet node has an entry in 'The Nodes of EMBnet' database which is available as Postscript format on nic.switch.ch in mirror/embnet-ch/info/embnet The embnet.dat file is a plain ASCII file and there are nice postscript versions with additional information as well. There is a Brasilian node in Brasilea which serves the community according to as imilar structure as the EMBnet nodes do in Europe, the Brazilian Molecular Biology and Biotechnology Network (BMBBNet). For more information, ask at ------------------------------------------------------------------------ | Goran Neshich | | | CENARGEN/EMBRAPA | e-mail: neshich@cenargen.embrapa.br | | S.A.I.N. Parque Rural, Final W5 | | | Asa Norte | Phone: +55 (61)273-0100 ext 127 | | 70770-900, Brasilia-D.F.-BRASIL | Fax: +55 (61)274-3212 | ------------------------------------------------------------------------ |> |> |> One of the numerous way is to use the UWGCG package, with the database |> Genembl. The option is TFASTA. This goes through the whole DNA database, TFASTA belongs to the FASTA package written by William R. Pearson originally described in Science (Lipman and Pearson, (1985) Science 227:1435-1441). The Genetics Computer Group, Inc. (Madison, Wisconsin) distributes a version which is adapted to their package. ... |> Software : UWGCG (University of Wisconsin Genetic Computer Group) it is |> available nearly everywhere there are molecular biology labs The package in question arose from an academic group (UWGCG) but is now comercially managed (Info at beers@gcg.com). Due to its history and economical factors, it is installed at a large basis. We have enjoyed excellent results arising from running this package since 1987. However, it is important to emphasize that other packages are available, such as the Intelligenetics Software Packahe (known as IG Suite, Info at ig-consultant@presto.ig.com), and others. There are many packages available from the public domain, though, these usually cover only a special (but very extensively covered) set of a particular activity, e.g. sequence searching, e.g., he FASTA was mentioned above, and the NCBI has released the 'BLAST' suite of programs. |> |> Database : Genembl, which is also from UWGCG, and is updated every 15 days (I think...) 'Genembl' is a term for a merged database used in the GCG package. On the basis of accession numbers, Genbank and EMBL are excluded in the corresponding database; e.g., in the US you would normally run GENBANK with a EMBL exclusion set, and in Europe you will have a EMBL with a Genbank exclusion set. The update frequency is a matter of your administrator, we do EMBL daily and GENBANK weekly, most sites in Switzerland maintain a weekly GCG GENEMBL data update. There oare other merged collections out there, PATCHX, OWL, and others. |> |> Time : well, this depends mainly on the machine you are using. It can range from 1hour to 15 min. BLAST (software from the NCBI) takes only a few seconds if peptide runs vs. peptice straight, and a Smith and Waterman search on a massively parallel machine (software from the Edinburgh team) doen't take longer either. The latter run on a deskside, 4 year old hardware might easily take 5 hours CPU to complete. The search software available ranges from scans of identity to sophisticated methods of fragment pattern searching, and from browsing the database with quick-but-dirty to extensive homology evaluations searching with profiles. ISEARCH (PIR), (T)FASTA (Pearson), BLAST (NCBI), WORDSEARCH(UWGCG), TWORDSEARCH(Rice), BLAZE (Intelligenetics), MPsearch(Collins et al, also as BLITZ), PROFILE methods (GRIBSKOV), FLASH (IBM), and many, many other programs have a wide area of application. So the range depends on * algorithm used * hardware used * question asked * (occasionally) length of the sequence Regards Reinhard -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ftp mirror at nic.switch.ch ----------------------------------------- From owner-proteins@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!lhc!borduas!francis From: francis@borduas.nlm.nih.gov (Francis Ouellette) Newsgroups: bionet.molbio.proteins Subject: Re: looking for proteins sequences Message-ID: <1993Dec5.151819.9686@nlm.nih.gov> Date: 5 Dec 93 15:18:19 GMT References: Sender: news@nlm.nih.gov Distribution: bionet Organization: National Library of Medicine Lines: 43 X-Newsreader: Tin 1.1 PL4 mcpalmie@FOX.CCE.USP.BR (Mauricio Cesar Palmieri) writes: : I have got a protein sequence and I would like to compare it with other : ones. Somebody there could tell me some information about how is the : easiest manner to proceed a roughly search? (database, software, time : required, etc). One (of many!) easy way to do it is to use the BLAST Email server at NCBI: blast@ncbi.nlm.nih.gov There are many databases you can querry there, and the best is to get the information document, which you can get by mailing to the server with the word 'help' in the body of the text (blank subject line). if you need help from a person (not a mail server), you can Email this address: info@ncbi.nlm.nih.gov : database Most of the major protein and nucleic acid databases are there. : software You need is an Email account. : time Depends on your Internet connection and the size of the querry, and how many other people are using the server at the same time you are. The search itself can take from a few seconds to a few minutes. regards, francis -- | B.F. Francis Ouellette | | francis@ncbi.nlm.nih.gov From owner-proteins@net.bio.net Mon Dec 06 22:00:00 1993 Path: biosci!relay.the.net!SHAUN%JASON.DECNET From: SHAUN%JASON.DECNET@relay.the.net ("Shaun D. Black") Newsgroups: bionet.molbio.proteins Subject: "Protein Folding" Message-ID: <01H65KKEDVSY000ZYQ@nic.the.net> Date: 6 Dec 93 15:31:09 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 11 Dear Colleagues, I am curious as to your comments on Tom Creighton's book, "Protein Folding" (W.H. Freeman, 1992). Which chapters were well written? Did it cover the folding problem accurately as of the time of publication? I am specially curious about your thoughts on the Introduction (chapter 1). Thanks for taking a few minutes to reply. I will summarize responses; this may generate some interesting topics for discussion. Cheers, Shaun =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = = Dept. of Biochemistry | University of Texas Health Center, at Tyler = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Mon Dec 06 22:00:00 1993 Path: biosci!JUDY.ENG.UCI.EDU!liang From: liang@JUDY.ENG.UCI.EDU (liang) Newsgroups: bionet.molbio.proteins Subject: CHINESES_BIOTECH_NET_FOUNDED Message-ID: <9312060501.AA19447@judy.eng.uci.edu> Date: 6 Dec 93 05:01:17 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 12 CBNet (Chinese Biotechnology Network) is a non-profit organization composed of professionals in biological, chemical, medical sciences, engineering and related fields. The CBNet sponsors the Chinese Biotechnology Internet Forum (CBIF) newsletter. To subscribe CBIF, please send an email to Listserv@UCSD.Edu with the message body: Add CB-Net. From owner-proteins@net.bio.net Mon Dec 06 22:00:00 1993 Path: biosci!JUDY.ENG.UCI.EDU!liang From: liang@JUDY.ENG.UCI.EDU (liang) Newsgroups: bionet.molbio.proteins Subject: CHINESES_BIOTECH_NET_FOUNDED Message-ID: <9312061946.AA20550@judy.eng.uci.edu> Date: 6 Dec 93 19:46:11 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 12 CBNet (Chinese Biotechnology Network) is a non-profit organization composed of professionals in biological, chemical, medical sciences, engineering and related fields. The CBNet sponsors the Chinese Biotechnology Internet Forum (CBIF) newsletter. To subscribe CBIF, please send an email to Listserv@UCSD.Edu with the message body: Add CB-Net. From owner-proteins@net.bio.net Tue Dec 07 22:00:00 1993 Path: biosci!FOX.CCE.USP.BR!szeinfel From: szeinfel@FOX.CCE.USP.BR (Rafael N Szeinfeld) Newsgroups: bionet.molbio.proteins Subject: Re: Internal repeats Message-ID: Date: 8 Dec 93 18:30:31 GMT References: <9312081718.AA20680@net.bio.net> Sender: daemon@net.bio.net Distribution: bionet Lines: 34 On 8 Dec 1993, Bob Lauder wrote: > > Hi, > > I have a protein, X, which contains a motif repeated several times within > the amino acid sequence. I also have the sequence of a couple of other > proteins, Y and Z, which share this internally repeated motif. > > What I'm after is the best way to find any other sequences which have > this repeated motif. It is a fairly short motif NxxNxNxxNxxN but is repeated > several (>9) times within a sequence of ~300aa. A search for the repeated motif > is probably is not the best way. So, any advice and suggestions, welcome. > > Bob. > > ============================================================================== > Bob Lauder, bsa016@cent1.lancs.ac.uk > Post Doctoral Research Associate, > Division of Biological Sciences, VOICE - (+44) (0)524 65201 Ex 3461 > Lancaster University, FAX - (+44) (0)524 843854 > U.K. > > Hi Bob, I'm curious to know why you use X,Y,Z and X on your message instead of real names. rafael najmanovich szeinfel@fox.cce.usp.br From owner-proteins@net.bio.net Tue Dec 07 22:00:00 1993 Path: biosci!daresbury!not-for-mail From: bsa016@cent1.lancs.ac.uk (Bob Lauder) Newsgroups: bionet.molbio.proteins Subject: Internal repeats Message-ID: <2e5283$j38@mserv1.dl.ac.uk> Date: 8 Dec 93 17:17:55 GMT Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Lines: 20 Original-To: proteins@dl.ac.uk Hi, I have a protein, X, which contains a motif repeated several times within the amino acid sequence. I also have the sequence of a couple of other proteins, Y and Z, which share this internally repeated motif. What I'm after is the best way to find any other sequences which have this repeated motif. It is a fairly short motif NxxNxNxxNxxN but is repeated several (>9) times within a sequence of ~300aa. A search for the repeated motif is probably is not the best way. So, any advice and suggestions, welcome. Bob. ============================================================================== Bob Lauder, bsa016@cent1.lancs.ac.uk Post Doctoral Research Associate, Division of Biological Sciences, VOICE - (+44) (0)524 65201 Ex 3461 Lancaster University, FAX - (+44) (0)524 843854 U.K. From owner-proteins@net.bio.net Tue Dec 07 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!library.ucla.edu!news.ucdavis.edu!chip.ucdavis.edu!ez005587 From: ez005587@chip.ucdavis.edu (David J. Meyer) Newsgroups: bionet.molbio.proteins Subject: Re: Secreted proteins Message-ID: Date: 8 Dec 93 16:22:52 GMT References: <1993Dec8.125241.20821@reks.uia.ac.be> Sender: usenet@ucdavis.edu (News Administrator) Organization: University of California, Davis Lines: 14 X-Newsreader: TIN [version 1.2 PL2] Przemko (przemko@reks.uia.ac.be) wrote: : Hi! : Can anyone tell me what % of proteins in an eukaryotic cell : is actually secreted and membrane bound? (stuff deleted) I, too, would be quite interested in any references addressing this question. It would also be interesting to see data comparing these values between different organisms! ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ David J. Meyer djmeyer@ucdavis.edu From owner-proteins@net.bio.net Tue Dec 07 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!EU.net!ub4b!reks.uia.ac.be!news From: przemko@reks.uia.ac.be (Przemko) Newsgroups: bionet.molbio.proteins Subject: Secreted proteins Message-ID: <1993Dec8.125241.20821@reks.uia.ac.be> Date: 8 Dec 93 12:52:41 GMT Sender: news@reks.uia.ac.be (USENET News System) Organization: University of Antwerp Lines: 14 X-Newsreader: Hi! Can anyone tell me what % of proteins in an eukaryotic cell is actually secreted and membrane bound? Depending on the source it could be 3% or 50%. But, all these numbers come from textbooks and I cannot find a paper (yeah, yeah I treid Medline...) where authors would actually try to quantify this distribution. Related to that would be what part of polysomes is membrane bound and what part not. I will greatly appreciate any insight and/or refs. I need it because I wonder if it is worthwhile to separate membrane-bound polysomes to enrich my library for secreted proteins or will that enrichement be to small to bother. ThanX Przemko From owner-proteins@net.bio.net Tue Dec 07 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!fnnews.fnal.gov!lakesis.fapesp.br!ime.usp.br!news From: fdcreina@quim.iq.usp.br Newsgroups: bionet.molbio.proteins Subject: crystal structure EDTA EGTA Message-ID: <2e4ecv$jif@mafalda.ime.usp.br> Date: 8 Dec 93 11:39:11 GMT Organization: Inst. Quimica USP Lines: 5 NNTP-Posting-Host: reina1.iq.usp.br Where can I get the coordinates for the crystal structure of EDTA, EGTA, EDTA-Ca, EGTA-Ca and EDTA-Mg ? Is there a way to do a ftp transfer from the Cambridge Structural Database? Thanks for the help. From owner-proteins@net.bio.net Tue Dec 07 22:00:00 1993 Path: biosci!ccs.carleton.ca!hmehrani From: hmehrani@ccs.carleton.ca (HOSSEIN MEHRANI) Newsgroups: bionet.molbio.proteins Subject: Doctoral position in Brazil, USP (fwd) Message-ID: <9312080831.AA28808@alfred.ccs.carleton.ca> Date: 8 Dec 93 08:31:42 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 37 HOSSEIN MEHRANI writes: From BIOSCI-REQUEST@net.bio.net Wed Dec 8 02:47:18 1993 From: hmehrani@ccs.carleton.ca (HOSSEIN MEHRANI) Message-Id: <9312080558.AA26340@alfred.ccs.carleton.ca> Subject: Doctoral position in Brazil, USP To: BIOSCI-REQUEST@net.bio.net Date: Wed, 8 Dec 93 0:58:24 EST Cc: immunology@net.bio.net X-Mailer: ELM [version 2.3 PL11] ATENTION (Brazilians only): ONE DOUTORAL POSITION AVAILABLE AT UNIVEERSITY OF SAO PAULO TO WORK WITH CHEMICAL MODELS OF INFLAMATION, THE ROLE OF OXYRADICALS AND IRON IONS. get in contact with Dr.Marcelo Hermes-Lima Departamento de Imunologia, ICB, USP Internet: hmehrani@ccs.carleton.ca FAX: 613-788-4389 I'm starting a new lab in march/abril and I'm looking for entusiastic canditates. We will apply for a CNPq or FAPESP fellowship. Sincerely: Dr.Marcelo H.-Lima xxsxxhxxxosxxxxxxxxxxxxxxxxxxxxxxxxxhxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxoxxu Other positions also available: Mestrado (1), Aperfeicoamento (3)3 , Postdoctoral fellow (1). "Iniciacao" (3) XCCXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX From owner-proteins@net.bio.net Tue Dec 07 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!warwick!pipex!uunet!nntp.club.cc.cmu.edu!cantaloupe.srv.cs.cmu.edu!das-news.harvard.edu!husc-news.harvard.edu!husc.harvard.edu!husc10!robison1 From: robison1@husc10.harvard.edu (Keith Robison) Newsgroups: bionet.molbio.proteins Subject: Re: Internal repeats Message-ID: Date: 8 Dec 93 20:20:44 GMT References: <2e5283$j38@mserv1.dl.ac.uk> Distribution: bionet Organization: Harvard University, Cambridge, Massachusetts Lines: 45 NNTP-Posting-Host: husc10.harvard.edu "Bob Lauder" writes: >Hi, > I have a protein, X, which contains a motif repeated several times within >the amino acid sequence. I also have the sequence of a couple of other >proteins, Y and Z, which share this internally repeated motif. > What I'm after is the best way to find any other sequences which have >this repeated motif. It is a fairly short motif NxxNxNxxNxxN but is repeated >several (>9) times within a sequence of ~300aa. A search for the repeated motif >is probably is not the best way. So, any advice and suggestions, welcome. Most sequence analysis packages have some sort of regular expression matching program -- the one in GCG is called FINDPATTERNS. There is also a freely available version of grep for sequences -- you should be able to find it using the software listing on the GDB gopher (gopher.gdb.org). You might also try browsing through SeqAnalRef on said gopher for other ftp-able pattern matching programs. Once you have found such a program, just ask it to find repeats of your pattern! For example, with FINDPATTERNS the pattern would be: (NxxNxNxxNxxN){2,} to match all things with at least two tandem copies of your repeat, and (NxxNxNxxNxxN)x{2,}(NxxNxNxxNxxN) to find two copies of your repeat with a variable length spacer. ( There's probably a more elegant way to write this one -- but this should be a working pattern). Once the pattern is defined, a typical workstation can search the protein databases in less than half a day. Enjoy! Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI krobison@nucleus.harvard.edu From owner-proteins@net.bio.net Tue Dec 07 22:00:00 1993 Path: biosci!relay.the.net!SHAUN%JASON.DECNET From: SHAUN%JASON.DECNET@relay.the.net ("Shaun D. Black") Newsgroups: bionet.molbio.proteins Subject: "Protein Folding" Message-ID: <01H68YBGTM0200140P@nic.the.net> Date: 9 Dec 93 01:34:14 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 15 Colleagues- Forgive the re-post if this actually made it to "Proteins", but our mailer has been on the blink lately and I have had no replies. >Dear Colleagues, > I am curious as to your comments on Tom Creighton's book, "Protein >Folding" (W.H. Freeman, 1992). Which chapters were well written? Did it >cover the folding problem accurately as of the time of publication? I am >specially curious about your thoughts on the Introduction (chapter 1). >Thanks for taking a few minutes to reply. I will summarize responses; this >may perhaps generate some interesting topics for discussion. Cheers, Shaun > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = > = Dept. of Biochemistry | University of Texas Health Center, at Tyler = > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From owner-proteins@net.bio.net Wed Dec 08 22:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!EU.net!uunet!munnari.oz.au!uniwa!uniwa!not-for-mail From: andrewh@uniwa.uwa.edu.au (Andrew Hobbs) Newsgroups: bionet.molbio.proteins Subject: Re: Secreted proteins Message-ID: <2e6tuf$omo@uniwa.uwa.edu.au> Date: 9 Dec 93 10:16:47 GMT References: <1993Dec8.125241.20821@reks.uia.ac.be> Organization: The University of Western Australia Lines: 33 NNTP-Posting-Host: uniwa.uwa.edu.au X-Newsreader: TIN [version 1.2 PL1] Przemko (przemko@reks.uia.ac.be) wrote: : Hi! : Can anyone tell me what % of proteins in an eukaryotic cell : is actually secreted and membrane bound? : Depending on the source it could be 3% or 50%. But, all these : numbers come from textbooks and I cannot find a paper (yeah, yeah Hi, Well I can't help you with a published paper but can give some figures. Quite a few years ago I found that about 90% of the ribosomes in rat mammary glands were in the form of membrane bound polysomes synthesising milk proteins. In the liver it was more like 30-40% were membrane bound. But both are very active in protein secretion. Surely both of the figures given above (3% and 50%) could be correct depending upon the cells or tissue involved. As for enriching libraries by posylsome purification, I certainly wouldn't try. Apart from anything else, the inevitable breakdown due to ribonuclease, means your cDNA clones will be even more partial than otherwise. My advice is forget it. Andrew Hobbs Biochemistry University of Western Australia andrewh@uniwa.uwa.edu.au : I treid Medline...) where authors would actually try : quantify this distribution. Related to that would be what : part of polysomes is membrane bound and what part not. : I will greatly appreciate any insight and/or refs. : I need it because I wonder if it is worthwhile to separate : membrane-bound polysomes to enrich my library for secreted proteins : or will that enrichement be to small to bother. : ThanX : Przemko From owner-proteins@net.bio.net Wed Dec 08 22:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!pipex!uunet!elroy.jpl.nasa.gov!sdd.hp.com!caen!batcomputer!ghost.dsi.unimi.it!genes!pongor From: pongor@genes.icgeb.trieste.it (Sandor Pongor) Newsgroups: bionet.molbio.proteins Subject: Mail server for protein functional domain homologies - ICGEB Trieste Keywords: mail server, molecular biology, protein domains, sequences Message-ID: <1993Dec9.100801.22225@genes.icgeb.trieste.it> Date: 9 Dec 93 10:08:01 GMT Organization: ICGEB Lines: 148 SS BBB A SS EEEE H H EEEE L PPP S S B B A A S S E H H E L P P S B B A A S E H H E L P P S BB AAAAA S EEE HHHHH EEE L PPP S B B A A S E H H E L P S B B A A S E H H E L P S S B B A A S S E H H E L P SSS BBB A A SSS EEEE H H EEEE LLLL P ---------------------------------- This is the help file of the SBASE Email Server at the International Centre for Genetic Engineering and Biotechnology AREA Science Park, Padriciano 99, 34012 Trieste, Italy. ---------------------------------- The SBASE Email Server is at present experimental. Please send comments to sbase-comment@icgeb.trieste.it. Thanks. The SBASE e-mail server accepts a specially formatted mail message containing a protein query sequence, and, as a response, it sends the list of the most probable domain homologies. A database search is performed against the SBASE library of protein domains using the BLAST algorithm, and the search results, provided with annotations, are returned in a mail message. How to use: Getting HELP: ============ This help file can be gotten by sending an email to sbase@icgeb.trieste.it containing the word HELP alone in the first line of the message body. Making a QUERY: =============== Send e-mail to sbase@icgeb.trieste.it using the below example Note: the parameters before the token BEGIN are optional, (here the defaults are listed), the lines after BEGIN are required. Example: MATRIX PAM120 SCORE PARAMETER 35 ANNOTATIONS YES BEGIN > mysequence LRNGVDINTCNQNGLNGLHLASKEGHVKMVVELLHKEIILETTTKKGNTALHIAALAGQDEVVRELVNYG GLNGLHLASKEGHVKMVVELLHKEIILETTTKKGNTALHIAALAGQDEVVRELVNYG Response time ============= Requests are handled immediately, in serial order. At present, response time is quite short and is restricted by the network load rather than CPU availability. Please note that large output files, such as sometimes occur with very short query sequences, may need a long time to traverse the net. Evaluation of the output: ========================= The output of the server are BLAST search results against the SBASE protein domain library. The output file contains the BLAST search results, organized as follows: 1) List of the best scoring domain entries. As SBASE entries are named by domain names (function, structure, etc.), this list already may give some information on the expected domain composition. 2) List of alignments. For each SBASE entry you will find the complete annotation of the domain, followed by one (or several) alignments with (different parts of) the query. If one domain is found several times in your query, you may find several alignments with the same or related entries at different parts of the query. Please note that it depends on the score parameter whether or not you see all the alignments. Do not use very low cutoff values because that results in prohibitively long output files. (For the time being, we have set the default cutoff to 35 and the minimum cutoff to 30). 3) Run statistics. This is usually not essential for the evaluation of the results; you can get a complete description of these and other blast parameters by sending a HELP message to blast.ncbi.nlm.nih.gov Important: Failure to see a homology with a known domain may be due to several reasons: i) The domain type is not (yet) included in the SBASE domain library; ii) The threshold score parameter was set too high for the domain to be detected; iii) A different scoring matrix may be necessary in order to detect the alignment with the domain type in question. In the present experimental version of the SBASE server we support only the matrices used by BLAST; "customized matrices" will be added later to the final version. Papers to reference in reporting results: ========================================= Pongor, S., Skerl, V., Cserzo, M. and Hatsagi, Z., Simon, G. and Bevilacqua, V. (1992): The SBASE domain library release 2.0& A collection of annotated protein sequence segments, Nucleic Acids. Res , 21, 311-315 Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman (1990) Basic local alignment search tool J. Mol. Biol. 215:403-410. Software availability ===================== The Sbase database is available by anonymous ftp at ftp.icgeb.trieste.it:/pub/sbase2 The blast software is available by anonymous ftp at ncbi.nlm.nih.gov:/pub/ Protection of your sequence data ================================ The query sequences are not stored in any form. Further info: ============= Server functions: Zsolt Hatsagi Tel: +39-40-3757342 Valeria Bevilacqua, systems manager (valeria@icgeb.trieste.it) Tel.: +39-40-3757330 General info: Sandor Pongor Tel: +39-40-3757300 FAX: +39-40-226-555 Mail: International Centre for Genetic Engineering and Biotechnology AREA Science Park, Padriciano 99 34012 Trieste, Italy From owner-proteins@net.bio.net Wed Dec 08 22:00:00 1993 Path: biosci!UNCVX1.OIT.UNC.EDU!KORTE From: KORTE@UNCVX1.OIT.UNC.EDU (JOHN) Newsgroups: bionet.molbio.proteins Subject: signal seq programs Message-ID: <01H69ZIXHV9E001B45@UNCVX1.OIT.UNC.EDU> Date: 9 Dec 93 18:23:19 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 6 Greetings, Does anyone have or know of a program that will allow me to predict the signal sequence polypeptides? I tried one on genbank called "ALOM" is there a better one perhaps? Or is there one witten for Macs or PC's? Thanks in advance, John Korte.... From owner-proteins@net.bio.net Wed Dec 08 22:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!EU.net!howland.reston.ans.net!newsserver.jvnc.net!netnews.upenn.edu!biochem.dental.upenn.edu!lally From: lally@biochem.dental.upenn.edu (Ned Lally) Newsgroups: bionet.molbio.proteins Subject: HELP:Nagase Message-ID: <2e7sa1$8dl@netnews.upenn.edu> Date: 9 Dec 93 18:54:57 GMT Organization: University of Pennsylvania Lines: 11 NNTP-Posting-Host: biochem.dental.upenn.edu I need help with the full name, address, phone and or fax number of Nagase ??, a Tokyo based Japanese chemical firm (I assume). Thanks bye, Ned _/_/_/_/ _/_/_/_/ _/ _/ _/ _/ Edward T. Lally _/ _/ _/ _/_/ _/ _/_/ _/ lally@biochem.dental.upenn.edu _/_/_/_/ _/_/_/ _/ _/ _/ _/ _/ _/ (215)898-5913|FAX(215)573-2050 _/ _/ _/ _/_/ _/ _/_/ The University of Pennsylvania _/ _/_/_/_/ _/ _/ _/ _/ (Not Penn State) From owner-proteins@net.bio.net Wed Dec 08 22:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!sunic!pipex!uunet!yeshua.marcam.com!zip.eecs.umich.edu!umn.edu!molbio.cbs.umn.edu!paul-b From: paul-b@molbio.cbs.umn.edu (Paul Bucciaglia) Newsgroups: bionet.molbio.methds-reagnts,bionet.molbio.proteins Subject: electrophoresis of plant proteins Message-ID: Date: 9 Dec 93 23:46:06 GMT Sender: news@news2.cis.umn.edu (Usenet News Administration) Organization: College of Biological Sciences, U of MN Lines: 25 Xref: biosci bionet.molbio.methds-reagnts:9793 bionet.molbio.proteins:1137 Nntp-Posting-Host: molbio.cbs.umn.edu Hello folks, I have been unhappy with the results of my plant protein PAGE gels for some time now and am looking for some suggestions. Let me start by stating what is working--electrophoresis of bacterial extracts or even pelleted cells or bugs straight out of culture boiled in loading buffer and electrophoresed on 4 --> 20 % gradient gels. this results in a crisp banding pattern when the gels are staine with Coomassie. I have been less succesful with protien extracts from leaves or stamens of tobacco. Usually I grind the tissue under lN2 in a mortar and pestle and add the frozen powder to tris (200mM pH 7.8) plus 14mM beta mercapto ethanol. The extracts are microcetrifuged and the supers removed to another tube. I add an equal amonunt of 2x load buffer (current proteocals in mol. biol recipe), boil 3', cool and load 10-20 microliters/well under the same buffer conditions that work great for bacterial proteins. The resulting gels lack the resolution and sharpness that I see in proteins from bacteria run under the same conditons on the same gels. So any suggestions? do I need to further purify my crude extracts of plant tissue? Are there any compounds which might cause the smearing and lack of resolution that I see in plant extracts? Any thoughts would be appreciated. paul bucciaglia From owner-proteins@net.bio.net Wed Dec 08 22:00:00 1993 Path: biosci!FOX.CCE.USP.BR!szeinfel From: szeinfel@FOX.CCE.USP.BR (Rafael N Szeinfeld) Newsgroups: bionet.molbio.proteins Subject: Re: "Protein Folding" Message-ID: Date: 9 Dec 93 11:19:07 GMT References: <01H68YBGTM0200140P@nic.the.net> Sender: daemon@net.bio.net Distribution: bionet Lines: 29 On 8 Dec 1993, Shaun D. Black wrote: > Colleagues- > Forgive the re-post if this actually made it to "Proteins", but our > mailer has been on the blink lately and I have had no replies. > > >Dear Colleagues, > > I am curious as to your comments on Tom Creighton's book, "Protein > >Folding" (W.H. Freeman, 1992). Which chapters were well written? Did it > >cover the folding problem accurately as of the time of publication? I am > >specially curious about your thoughts on the Introduction (chapter 1). > >Thanks for taking a few minutes to reply. I will summarize responses; this > >may perhaps generate some interesting topics for discussion. Cheers, Shaun > > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > > = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = > > = Dept. of Biochemistry | University of Texas Health Center, at Tyler = > > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > Hi Shaun, I'm begining to read it now but I already read the first chapter. I though interesting the non-biologist aproach he used as usualy people deal with the subject mainly when he talks about some concepts on polymer chemistry. rafael najmanovich szeinfel@fox.cce.usp.br From owner-proteins@net.bio.net Thu Dec 09 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!saimiri.primate.wisc.edu!caen!batcomputer!ghost.dsi.unimi.it!univ-lyon1.fr!jussieu.fr!univ-lille1.fr!cict.fr!ecstasy!maveyrau From: maveyrau@ecstasy.NoSubdomain.NoDomain (Laurent Maveyraud) Newsgroups: bionet.molbio.proteins Subject: Protein Concentration ? Message-ID: <2eapkr$1qa@reseau.cict.fr> Date: 10 Dec 93 21:27:55 GMT Sender: maveyrau@ecstasy (Laurent Maveyraud) Organization: Laboratoire de Pharmacologie et Toxicologie Fondamentales (LPTF/CNRS, Toulouse) Lines: 12 NNTP-Posting-Host: 192.93.13.7 We have a problem about protein concentration determination. We have a pure protein, but we are unable to determine its concentration by usual methods (optical density at 280nm and Bradford assays). Can anybody give us references about other methods to determine protein concentration, or any suppliers which can provide us with this kind of kit (european address will be more usefull, but send whatever you can). I would prefer any answer by direct e-mail. If anybody is interested, I will put a summary on this list. Many thanks Laurent Maveyraud, Groupe de cristallographie du LPTF, CNRS maveyrau@cemes.fr From owner-proteins@net.bio.net Thu Dec 09 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!news.claremont.edu!nntp-server.caltech.edu!robin From: robin@cco.caltech.edu (Robert C. Colgrove) Newsgroups: bionet.molbio.proteins Subject: Re: signal seq programs Message-ID: <2ea6mc$f5m@gap.cco.caltech.edu> Date: 10 Dec 93 16:04:28 GMT References: <01H69ZIXHV9E001B45@UNCVX1.OIT.UNC.EDU> Distribution: bionet Organization: California Institute of Technology, Pasadena Lines: 15 NNTP-Posting-Host: alumni.caltech.edu KORTE@UNCVX1.OIT.UNC.EDU (JOHN) writes: >Greetings, > Does anyone have or know of a program that will allow me to predict the >signal sequence polypeptides? I tried one on genbank called "ALOM" is there a >better one perhaps? Or is there one witten for Macs or PC's? > Thanks in advance, > John Korte.... I posted a C program that implements the von Heijne algorithm a while back. If there is enough interest I will repost or if there is a convenient archive we can put it there. cheers robin colgrove@xtal10.harvard.edu From owner-proteins@net.bio.net Thu Dec 09 22:00:00 1993 Path: biosci!MBCMAIL.AB.UMD.EDU!collins From: collins@MBCMAIL.AB.UMD.EDU (John Collins) Newsgroups: bionet.molbio.proteins Subject: protein sequencing lab Message-ID: <9312101435.A03094@mbcmail.ab.umd.edu> Date: 10 Dec 93 19:35:05 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 43 ---------------------------------- Forwarded ---------------------------------- From: John Collins Date: 12/10/93 2:18PM To: John Collins Subject: protein sequencing lab ------------------------------------------------------------------------------- Dear Colleague: I would like to call to your attention the availability of the PROTEIN SEQUENCING LAB, a core facility of the University of Maryland. We offer: PROTEIN/PEPTIDE SEQUENCING AMINO ACID ANALYSIS PEPTIDE MAPPING AND PURIFICATION BY HPLC IDENTIFICATION OF MODIFIED AMINO ACIDS DATABASE HOMOLOGY SEARCHES SECONDARY STRUCTURE PREDICTIONS HYDROPATHY PROFILES CONFIDENTIALITY EXPERIENCED, HELPFUL STAFF PERSONAL ATTENTION CONSULTATIONS PROPOSAL WRITING ASSISTANCE COLLABORATIONS FAST, QUALITY SERVICE COMPETITIVE PRICES Our mailing address is: Dr. John H. Collins Protein Sequencing Lab Dept. of Biological Chemistry Univ. Maryland School of Medicine 108 N. Greene St. Baltimore, MD 21201 For further information contact me, the lab director, John H. Collins, Ph.D., Professor of Medical Biotechnology and Biological Chemistry. tel: (410) 706-8102 fax: (410) 706-7364 e-mail: collins@mbcmail.ab.umd.edu From owner-proteins@net.bio.net Fri Dec 10 22:00:00 1993 Path: biosci!GPU.SRV.UALBERTA.CA!ghawkins From: ghawkins@GPU.SRV.UALBERTA.CA (Glen Hawkins) Newsgroups: bionet.molbio.proteins Subject: Re: Protein Concentration ? Message-ID: Date: 11 Dec 93 18:42:10 GMT References: <9312102042.AA26180@net.bio.net> Sender: daemon@net.bio.net Distribution: bionet Lines: 24 On 10 Dec 1993, Laurent Maveyraud wrote: > Date: 10 Dec 93 21:27:55 GMT > From: Laurent Maveyraud > To: proteins@net.bio.net > Subject: Protein Concentration ? > > > We have a problem about protein concentration determination. We have a pure protein, but we are unable to determine its concentration by usual methods (optical density at 280nm and Bradford assays). > > Can anybody give us references about other methods to determine protein concentration, or any suppliers which can provide us with this kind of kit (european address will be more usefull, but send whatever you can). > > I would prefer any answer by direct e-mail. If anybody is interested, I will put a summary on this list. > > Many thanks > > > Laurent Maveyraud, Groupe de cristallographie du LPTF, CNRS > maveyrau@cemes.fr > > check methods in enzymology vol 182. This list several different methods in determining protein concentration such as; absorbance @ 205 nm. From owner-proteins@net.bio.net Sun Dec 12 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!EU.net!sunic!trane.uninett.no!nntp.uio.no!usenet From: LESZEK@BIOMED.UIO.NO (Leszek Kleczkowski) Newsgroups: bionet.molbio.proteins Subject: Re: plastid transit peptide program? Date: 13 Dec 1993 15:35:49 GMT Organization: NORWEGIAN EMBNET NODE Lines: 11 Distribution: world Message-ID: <2ei24l$bsh@hermod.uio.no> References: <2ei1sp$bsh@hermod.uio.no> NNTP-Posting-Host: biomed.uio.no X-News-Reader: VMS NEWS 1.24 In-Reply-To: LESZEK@BIOMED.UIO.NO's message of 13 Dec 1993 15:31:37 GMT In <2ei1sp$bsh@hermod.uio.no> LESZEK@BIOMED.UIO.NO writes: Sorry for my messed-up previous message. The correct one is: I just wonder whether anybody can recommend a computer program for recognition of transit peptide sequence for nuclear-encoded plastid-based plant proteins (based on cDNA-derived amino acid sequence). Thanx Leszek From owner-proteins@net.bio.net Sun Dec 12 22:00:00 1993 Newsgroups: bionet.molbio.proteins Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!pipex!sunic!EU.net!ub4b!reks.uia.ac.be!news From: przemko@reks.uia.ac.be (Przemko) Subject: Re: signal seq programs Message-ID: <1993Dec13.090141.28088@reks.uia.ac.be> Sender: news@reks.uia.ac.be (USENET News System) Organization: University of Antwerp X-Newsreader: Date: Mon, 13 Dec 1993 09:01:41 GMT Lines: 20 In article <2ea6mc$f5m@gap.cco.caltech.edu> robin@cco.caltech.edu (Robert C. Colgrove) writes: >KORTE@UNCVX1.OIT.UNC.EDU (JOHN) writes: > >>Greetings, >> Does anyone have or know of a program that will allow me to predict the >>signal sequence polypeptides? I tried one on genbank called "ALOM" is there a >>better one perhaps? Or is there one witten for Macs or PC's? >> Thanks in advance, >> John Korte.... > >I posted a C program that implements the von Heijne algorithm a while back. >If there is enough interest I will repost or if there is a convenient archive >we can put it there. >cheers >robin >colgrove@xtal10.harvard.edu > Yes, please put it somwhere. It is not for Win, by any chance? ThanX Przemko From owner-proteins@net.bio.net Sun Dec 12 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!cs.utexas.edu!howland.reston.ans.net!pipex!sunic!trane.uninett.no!nntp.uio.no!usenet From: LESZEK@BIOMED.UIO.NO (Leszek Kleczkowski) Newsgroups: bionet.molbio.proteins Subject: plastid transit peptide program? Date: 13 Dec 1993 15:31:37 GMT Organization: NORWEGIAN EMBNET NODE Lines: 7 Distribution: world Message-ID: <2ei1sp$bsh@hermod.uio.no> NNTP-Posting-Host: biomed.uio.no X-News-Reader: VMS NEWS 1.24 recognition of transit peptide sequence for nuclear-encoded plastid-based plant proteins (based on cDNA-derived amino acid sequence). Thanx Leszek From owner-proteins@net.bio.net Sun Dec 12 22:00:00 1993 Newsgroups: bionet.molbio.proteins Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!pipex!uknet!gdt!aber!spp From: spp@aber.ac.uk (Simon Peter Penson) Subject: Plant sucrase antibody Message-ID: <1993Dec13.123526.10271@aber.ac.uk> Sender: Simon Penson (spp@aber.ac.uk) Organization: University of Wales, Aberystwyth Date: Mon, 13 Dec 1993 12:35:26 GMT Lines: 7 I'm trying to find ouy if there is an antibody to plant sucrase proteins (specifically wheat or barley). Alternatively, does anyone know of a bacterial antibody exists? Cheers Simon Penson. From owner-proteins@net.bio.net Sun Dec 12 22:00:00 1993 Path: biosci!daresbury!not-for-mail From: "Andrew, Tel. +39-6-91093434" Newsgroups: bionet.molbio.proteins Subject: Re: Protein Concentration ? Date: 13 Dec 1993 11:07:22 -0000 Lines: 21 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2ehida$lth@mserv1.dl.ac.uk> Original-To: proteins@dl.ac.uk In reply to the message Laurent Maveyraud sent: > Date: 10 Dec 93 21:27:55 GMT > From: Laurent Maveyraud > To: proteins@net.bio.net > Subject: Protein Concentration ? > > > We have a problem about protein concentration determination. We have a pure > protein, but we are unable to determine its concentration by usual methods > (optical density at 280nm and Bradford assays). .............(Stuff deleted) Other possibilities would be to try the Biuret method, the Lowry procedure or bicinchoninic acid method (Smith et al., (1985) Analytical Biochem. 150, 76 ff. Protocols for these methods can be found in the Practical Approach series book "Protein Purification Methods" edited by E.L.V. Harris and S. Angal (1989) from IRL Press. Andrew Wallace, IRBM P. Angeletti, Pomezia, Italy From owner-proteins@net.bio.net Sun Dec 12 22:00:00 1993 Path: biosci!hubcap!darwin.sura.net!gatech!europa.eng.gtefsd.com!uunet!noc.near.net!saturn.caps.maine.edu!dartvax.dartmouth.edu!James.F.X.Wellehan From: James.F.X.Wellehan@dartmouth.edu (Jim Wellehan) Newsgroups: bionet.general Subject: Re: a.calcoaceticus - what is it ? Date: 13 Dec 1993 18:31:02 GMT Organization: Dartmouth College, Hanover, NH Lines: 4 Message-ID: <2eicd6$5t6@dartvax.dartmouth.edu> References: <1993Dec13.145524.12941@infodev.cam.ac.uk> NNTP-Posting-Host: at-sn-284.dartmouth.edu X-Posted-From: InterNews 1.0@dartmouth.edu Sorry for posting, but I tried to mail you & it bounced. Acinetobacter calcoaceticus is a gram-negative coccobacillus. Jim From owner-proteins@net.bio.net Sun Dec 12 22:00:00 1993 Path: biosci!bcm!avdms8.msfc.nasa.gov!europa.eng.gtefsd.com!howland.reston.ans.net!news.intercon.com!uhog.mit.edu!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!athena.mit.edu!dresnick From: dresnick@athena.mit.edu (David I Resnick) Newsgroups: bionet.molbio.proteins Subject: Re: Protein Concentration ? Date: 14 Dec 1993 01:54:26 GMT Organization: Massachusetts Institute of Technology Lines: 22 Distribution: bionet Message-ID: References: <2ehida$lth@mserv1.dl.ac.uk> NNTP-Posting-Host: pesto.mit.edu In-reply-to: "Andrew, Tel. +39-6-91093434"'s message of 13 Dec 1993 11:07:22 -0000 In article <2ehida$lth@mserv1.dl.ac.uk> "Andrew, Tel. +39-6-91093434" writes: In reply to the message Laurent Maveyraud sent: > Date: 10 Dec 93 21:27:55 GMT > From: Laurent Maveyraud > To: proteins@net.bio.net > Subject: Protein Concentration ? > > > We have a problem about protein concentration determination. We have a pure > protein, but we are unable to determine its concentration by usual methods > (optical density at 280nm and Bradford assays). .............(Stuff deleted) How about having an amino acid analysis done? At MIT this costs $25 and is a pretty accurate way of measuring the concentration of your protein. Of course, you wouldn't want to use this every day, but it is certainly a nice way of calibrating whatever spectophotometric based assay you settle on. (This assumes you have enough to waste on aaa, but it doesn't really take THAT much to do it). -- David Resnick dresnick@athena.mit.edu From owner-proteins@net.bio.net Mon Dec 13 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!caen!batcomputer!ghost.dsi.unimi.it!univ-lyon1.fr!news.imag.fr!ciril.fr!mouze From: mouze@ciril.fr (Marc Mouze-Amady) Newsgroups: bionet.molbio.methds-reagnts Subject: any experience with salivary cytokines? Date: 14 Dec 1993 09:28:27 GMT Organization: CIRIL, Nancy, France Lines: 20 Message-ID: <2ek0vr$rma@arcturus.ciril.fr> NNTP-Posting-Host: hp825.inrs.fr X-Newsreader: TIN [version 1.1 PL9] [ Article crossposted from bionet.immunology ] [ Author was Marc Mouze-Amady ] [ Posted on 14 Dec 1993 08:47:49 GMT ] Hello bionetters, I am looking for references on cytokines excreted into saliva. Any help would be appreciated.Thanks in advance. Marc. +=======================================================+ + Marc MOUZE-AMADY PhD + Voice : 33-83.50.20.00 + + I.N.R.S. + ext. 25.28 + + Environ. Physiol. dept. +========================+ + Occupational Physiol. lab. + Fax : 33-83.50.20.19 + + B.P. 27 + 33-83.50.20.97 + + F-54501 Vandoeuvre cedex +========================+ + FRANCE + E.mail: mouze@inrs.fr + +=======================================================+ ....................................................... From owner-proteins@net.bio.net Mon Dec 13 22:00:00 1993 Path: biosci!bloom-beacon.mit.edu!news.kei.com!sol.ctr.columbia.edu!howland.reston.ans.net!usenet.ins.cwru.edu!lerc.nasa.gov!purdue!mentor.cc.purdue.edu!inet.d48.lilly.com!mcvax4.d48.lilly.com!dallas Newsgroups: bionet.molbio.methds-reagnts Subject: Re: NDOWName a clone? Message-ID: <1993Dec13.153305.1@mcvax4.d48.lilly.com> From: dallas@mcvax4.d48.lilly.com Date: 13 Dec 93 15:33:05 EST References: <9312092255.AA14481@fraser.sfu.ca> <1993Dec10.183640.1@molbiol.ox.ac.uk> Distribution: bionet,world Nntp-Posting-Host: mcvax4.d48.lilly.com Lines: 41 In article , paul-b@molbio.cbs.umn.edu (Paul Bucciaglia) writes: >>In article <9312092255.AA14481@fraser.sfu.ca>, peijunz@sfu.ca writes: >>> Hi netters, >>> When you got a clone (cDNA clone or genomic DNA clone), you need to >>> name it. I was wondering if there is any rule to do this. I recently got >>> a cDNA clone of cysteine proteinase from wheat (my insert is in >>> pBluescript). What name could I give to my clone? >>> >>Why not pPZ... Lots of people name their clone after themselves! >> >>Iain Wilson >>iwilson@molbiol.ox.ac.uk > > No flame/malice/busting intended but it is much more informative if you > give the clone a name which reflects its function, expresion pattter etc. > I am not very imaginative but you could do something like "cpw" for > "Cysteine Proteinase from Wheat" or "cyp" for "CYsteine Proteinase". > Others may have better suggestions; its just more helpful to the reader > of a paper if they can connect the name of your clone to something > biologically relevant. > > paul bucciaglia > Back in the seventies and early eighties, there actually was a cataloguing of plasmid names that used two and three letter codes followed by a number. E. g. pMF1...2...3 which, of course, stood for Mayo Foundation. Esther Lederberg at Stanford used to keep this list. Since there weren't many two letter codes left, I took "OW" which gave my plasmid, cDNA, and viral DNA's pOW, cOW, and vOW #'s. Cute, uh? :-\ I believe in the descriptive idea however, and unless they get mixed up in the lab can be very helpful in calling to mind constructions that may be several years old, especially if they led to publication. I usually describe the most important part, the insert, with a series of plasmids that have a particular promoter, or signal sequence, or ... . By all means, be creative!!! JIm Miller Lilly Research Labs From owner-proteins@net.bio.net Mon Dec 13 22:00:00 1993 Newsgroups: bionet.molbio.proteins Path: biosci!lhc!darwin.sura.net!howland.reston.ans.net!pipex!uknet!gdt!aber!spp From: spp@aber.ac.uk (Simon Peter Penson) Subject: RE: Electrophoresis of plant proteins Message-ID: <1993Dec14.171132.17145@aber.ac.uk> Sender: Simon Penson (spp@aber.ac.uk) Organization: University of Wales, Aberystwyth Distribution: bionet.molbio.proteins, bionet.plants Date: Tue, 14 Dec 1993 17:11:32 GMT Lines: 11 Seeing as several people seem to have had problems when changing form microbes to the real world of plants [;-)], I thought I'd chip in. I regularly run gels (native and sds) on a variety of plant protein preps. The best way to avoid horrible contaminats is to desalt the protein prior to electrophoresis. I use the Biorad gels (eg P6-DG) in syringe barrels as spin-desalting columns. Works a treat! Simon Penson. From owner-proteins@net.bio.net Mon Dec 13 22:00:00 1993 Path: biosci!daresbury!not-for-mail From: yduroche@popserver.ens-lyon.fr (Yves Durocher) Newsgroups: bionet.molbio.proteins Subject: Removing nucleic acids from protein samples Date: 14 Dec 1993 17:14:59 -0000 Lines: 8 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2eksaj$d0v@mserv1.dl.ac.uk> Original-To: proteins@dl.ac.uk content-length: 351 Is there a simple method to efficiently remove nucleic acids from [SDS-PAGE sample buffer]-solubilized cells? I have a lot of problems to see high molecular weight proteins after SDS-PAGE because of smears probably due to DNA and RNA. To method should remove as little as possible proteins from the sample. Thanks in advance... Yves Durocher From owner-proteins@net.bio.net Mon Dec 13 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!emory!emoryu1!emoryu1.cc.emory.edu From: clarsen@emoryu1.cc.emory.edu (Chris Larsen) Newsgroups: bionet.molbio.proteins Subject: Re: Pre-staining of MW markers Message-ID: <6093@emoryu1.cc.emory.edu> Date: 14 Dec 93 20:41:33 GMT References: Sender: news@emory.edu Reply-To: clarsen@emoryu1.cc.emory.edu Organization: Emory University (BIMCORE) Lines: 7 Nntp-Posting-Host: emoryu1.cc.emory.edu Sigma has a set of prestained markers which have been shown to migrate at 26,36,48,58,84,116,and180 kDa. We find them very accurate and easy to use... It is called SDS-7B. Chris From owner-proteins@net.bio.net Mon Dec 13 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!agate!mendel.Berkeley.EDU!genecutl From: genecutl@mendel.Berkeley.EDU ( Gene Cutler) Newsgroups: bionet.molbio.proteins Subject: Re: Removing nucleic acids from protein samples Date: 14 Dec 1993 20:52:02 GMT Organization: /etc/organization Lines: 26 Distribution: bionet Message-ID: <2el91i$q9f@agate.berkeley.edu> References: <2eksaj$d0v@mserv1.dl.ac.uk> NNTP-Posting-Host: mendel.berkeley.edu In article <2eksaj$d0v@mserv1.dl.ac.uk>, Yves Durocher wrote: > Is there a simple method to efficiently remove nucleic acids from >[SDS-PAGE sample buffer]-solubilized cells? I have a lot of problems to see >high molecular weight proteins after SDS-PAGE because of smears probably >due to DNA and RNA. To method should remove as little as possible proteins >from the sample. >Thanks in advance... >Yves Durocher > Polyamine P precipitation. It precipitates nucleic acids (and anything bound to them) while leaving proteins alone. (I don't have a protocol, though, so this is as much as I can help you) -gc From owner-proteins@net.bio.net Tue Dec 14 22:00:00 1993 Newsgroups: bionet.molbio.proteins Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!darwin.sura.net!gatekeeper.es.dupont.com!esds01.es.dupont.com!MILLERTJ@esvx17.es.dupont.com From: millertj@esvx17.es.dupont.com (Thomas Miller, Dupont, Wilm, DE) Subject: Porton / Beckman protein sequencer users Message-ID: <1993Dec15.143148.22181@es.dupont.com> Sender: news@es.dupont.com (USENET News System) Nntp-Posting-Host: esvx17.es.dupont.com Reply-To: millertj@esvx17.es.dupont.com Organization: DuPont (Opinions are those of the writer only) Date: Wed, 15 Dec 1993 14:31:48 GMT Lines: 8 I am interested in compiling a list of Porton / Beckman protein sequencer users. If you would like to be included, please send e-mail to millertj@esvax.dnet.dupont.com . There are no commercial overtones to this request. I just thought we could get an informal group together to talk shop, techniques, complaints, etc. I am not aware of anything like this being formed. Thank you. Tom. From owner-proteins@net.bio.net Tue Dec 14 22:00:00 1993 Newsgroups: bionet.molbio.proteins Path: biosci!bloom-beacon.mit.edu!news.kei.com!sol.ctr.columbia.edu!howland.reston.ans.net!europa.eng.gtefsd.com!library.ucla.edu!news.ucdavis.edu!othello.ucdavis.edu!ez002976 From: ez002976@othello.ucdavis.edu () Subject: BASIC CHITINASE ANTIBODY ? Message-ID: Keywords: chitinase antibody cucumber Sender: usenet@ucdavis.edu (News Administrator) Organization: University of California, Davis X-Newsreader: TIN [version 1.2 PL2] Date: Wed, 15 Dec 1993 15:49:46 GMT Lines: 12 Hello all : I'm looking for a basic chitinase antibody which might cross react with extracellular proteins I am purifying from plant tissue culture extracts of chinese cucumber. I'd appreciate any information or leads to a source for the above. thanks in advance Nishant email :nbhatia@ucdavis.edu From owner-proteins@net.bio.net Tue Dec 14 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!news.claremont.edu!nntp-server.caltech.edu!robin From: robin@cco.caltech.edu (Robert C. Colgrove) Newsgroups: bionet.general,bionet.molbio.proteins,bionet.software Subject: C code for Von Heijne signal sequence algorithm Date: 15 Dec 1993 17:42:34 GMT Organization: California Institute of Technology, Pasadena Lines: 315 Message-ID: <2eniaa$q07@gap.cco.caltech.edu> NNTP-Posting-Host: alumni.caltech.edu Xref: biosci bionet.general:6818 bionet.molbio.proteins:1148 bionet.software:6746 Hi bionetters. I got so many requests for the signal sequence program I mentioned that I will repost it. Feel free to use, distribute or archive. Just send me email if you do and cite the program as, "Colgrove, RC, PhD Dissertation, UCSF dept of Biochemistry, 1990." This program implements the Von Heijne algorithm to find potential signal sequences (reference is at the end of the code). It does a very good job at finding real signals, even internal and atypical signals. I have used it to: -provide evidence that some newly cloned gene encode a secreted protein -identify weak of unusual internal signal sequences -identify mutations that would likely affect secretion -examine the statistical distribution of signal sequences in real protein sequences and in random sequences. The program with called with no arguments prints the matrices used and the Von Heijne reference. With one argument, it reads that argument as a file name containing a one-letter amino acid code and prints to the standard output one line for each residue showing the residue number, the one-letter code, and a score for how likely a peptidase site that position would be. At the last line, it prints the position of the best site and its score and tells whether it is a likely signal. To plot a graph of the scores, calling the program with an extra dummy argument (eg signal filename dummyarg) produces output that can be piped to UNIX plot and graph. For example the script: signal $1 s > infile graph -l "signal sequence profile for "$1 < infile | plot -T4014 > outfile cat outfile rm infile outfile makes a nice graph of the signal sequence profile ofthe filename given in $1. I have also included the code for a variant of the program, signal.filtered, which prints a zero score for all poor signal positions. This produces a much prettier graph where only the signals show up as clean spikes. I have only run these programs on UNIX machine but the C code should be portable to anything. Good luck and by all means let me know if you find these useful. -robin RC Colgrove colgrove@xtal10.harvard.edu :::::::::::::::::::::::::::::::::::::::::::::::: signal.c ::::::::::::::::::::::::::::::::::::::::::::::: #include #include #define aminotype "ACDEFGHIKLMNPQRSTVWY" #define SAMPLE 450 #define seqfile argv[1] float expect[] = {14.5,4.5,8.9,10.0,5.6,12.1,3.4,7.4,11.3,12.1, 2.7,7.1,7.4,6.3,7.6,11.4,9.7,11.1,1.8,5.6}; float freq[20][15] = { 16,13,14,15,20,18,18,17,25,15,47,6,80,18,6, 3,6,9,7,9,14,6,8,5,6,19,3,9,8,3, 0,0,0,0,0,0,0,0,5,3,0,5,0,10,11, 0,0,0,1,0,0,0,0,3,7,0,7,0,13,14, 13,9,11,11,6,7,18,13,4,5,0,13,0,6,4, 4,4,3,6,3,13,3,2,19,34,5,7,39,10,7, 0,0,0,0,0,1,1,0,5,0,0,6,0,4,2, 15,15,8,6,11,5,4,8,5,1,10,5,0,8,7, 0,0,0,1,0,0,1,0,0,4,0,2,0,11,9, 71,68,72,79,78,45,64,49,10,23,8,20,1,8,4, 0,3,7,4,1,6,2,2,0,0,0,1,0,1,2, 0,1,0,1,1,0,0,0,3,3,0,10,0,4,7, 2,0,2,0,0,4,1,8,20,14,0,1,3,0,22, 0,0,0,1,0,6,1,0,10,8,0,18,3,19,10, 2,0,0,0,0,1,0,0,7,4,0,15,0,12,9, 9,3,8,6,13,10,15,16,26,11,23,17,20,15,10, 2,10,5,4,5,13,7,7,12,6,17,8,6,3,10, 20,25,15,18,13,15,11,27,0,12,32,3,0,8,17, 4,3,3,1,1,2,5,3,1,3,0,9,0,2,0, 0,1,4,0,0,1,3,1,1,2,0,5,0,1,7 }; main(argc,argv) int argc; char *argv[]; { int i,j,k,shift; float weight[20][15],score[1000],max; FILE *fp, *fopen(); char c, seqbuff[15]; if(argc==1) { printf("\n\t\tSIGNAL SEQUENCE FINDER\n"); printf("\n\nFREQUENCY MATRIX\n\n"); printf("\t"); for(i=0;i<16;i++) { if(i>3) printf(" "); if(i>12) printf(" "); if(i==13) i++; printf("%d ",i-13); } printf("\tEXPECT\n\n"); for(j=0;j<20;j++) { printf("%c\t",aminotype[j]); for(i=0;i<15;i++) printf(" %2.0f ",freq[j][i]); printf("\t%4.1f\n",expect[j]); } } for(j=0;j<20;j++) { for(i=0;i<15;i++) { if(freq[j][i]==0) { freq[j][i]=1; if(i==10||i==12) freq[j][i]=expect[j]/SAMPLE; } weight[j][i]=log(freq[j][i]/expect[j]); } } if(argc==1) { printf("\n\nWEIGHT MATRIX (x 100)\n\n"); printf(" "); for(i=0;i<16;i++) { if(i>3) printf(" "); if(i>12) printf(" "); if(i==13) i++; printf(" %d",i-13); } printf("\n\n"); for(j=0;j<20;j++) { printf("%c ",aminotype[j]); for(i=0;i<15;i++) printf("%4.0f ",100*(weight[j][i])); printf("\n"); } printf("\nmethod from: Gunnar von Heijne, NAR 14, p.4683, 1986\n"); } if(argc!=1) { if((fp=fopen(seqfile,"r"))==NULL) printf("no such file\n"); if(argc==2) printf("\n\nSCORE PROFILE of %s\n\ncleave\tscore\tresidue\n\n",seqfile); while((c=getc(fp))!=EOF&&c!=NULL) { if(c==' '||c=='\t'||c=='\n') continue; seqbuff[14]=c; for(i=0;i<15;i++) for(j=0;j<20;j++) if(seqbuff[i]==aminotype[j]) score[k] += weight[j][i]; if(score[k]>max) { max=score[k]; shift=k; } printf("%d\t%4.2f",k-1,score[k]); if(argc==2) printf("\t%c",seqbuff[12]); printf("\n"); for(i=0;i<14;i++) seqbuff[i]=seqbuff[i+1]; k++; } if(argc==2) { printf("\nmax score is %4.2f, cleaved after res %d\n\n",max,shift-1); if(max<0.0) printf("improbable signal sequence\n"); if(max>=0.0&&max<5.0) printf("possible but ambiguous signal\n"); if(max>=5.0&&max<10.0) printf("probable signal sequence\n"); if(max>=10.0) printf("highly probable signal sequence\n"); } } } ::::::::::::::::::::::::::::::::::::::::::::::::::::::;;; signal.filtered.c :::::::::::::::::::::::::::::::::::::::::::::::::::::::: #include #include #define aminotype "ACDEFGHIKLMNPQRSTVWY" #define SAMPLE 450 #define seqfile argv[1] float expect[] = {14.5,4.5,8.9,10.0,5.6,12.1,3.4,7.4,11.3,12.1, 2.7,7.1,7.4,6.3,7.6,11.4,9.7,11.1,1.8,5.6}; float freq[20][15] = { 16,13,14,15,20,18,18,17,25,15,47,6,80,18,6, 3,6,9,7,9,14,6,8,5,6,19,3,9,8,3, 0,0,0,0,0,0,0,0,5,3,0,5,0,10,11, 0,0,0,1,0,0,0,0,3,7,0,7,0,13,14, 13,9,11,11,6,7,18,13,4,5,0,13,0,6,4, 4,4,3,6,3,13,3,2,19,34,5,7,39,10,7, 0,0,0,0,0,1,1,0,5,0,0,6,0,4,2, 15,15,8,6,11,5,4,8,5,1,10,5,0,8,7, 0,0,0,1,0,0,1,0,0,4,0,2,0,11,9, 71,68,72,79,78,45,64,49,10,23,8,20,1,8,4, 0,3,7,4,1,6,2,2,0,0,0,1,0,1,2, 0,1,0,1,1,0,0,0,3,3,0,10,0,4,7, 2,0,2,0,0,4,1,8,20,14,0,1,3,0,22, 0,0,0,1,0,6,1,0,10,8,0,18,3,19,10, 2,0,0,0,0,1,0,0,7,4,0,15,0,12,9, 9,3,8,6,13,10,15,16,26,11,23,17,20,15,10, 2,10,5,4,5,13,7,7,12,6,17,8,6,3,10, 20,25,15,18,13,15,11,27,0,12,32,3,0,8,17, 4,3,3,1,1,2,5,3,1,3,0,9,0,2,0, 0,1,4,0,0,1,3,1,1,2,0,5,0,1,7 }; main(argc,argv) int argc; char *argv[]; { int i,j,k,shift; float weight[20][15],score[1000],max; FILE *fp, *fopen(); char c, seqbuff[15]; if(argc==1) { printf("\n\t\tSIGNAL SEQUENCE FINDER\n"); printf("\n\nFREQUENCY MATRIX\n\n"); printf("\t"); for(i=0;i<16;i++) { if(i>3) printf(" "); if(i>12) printf(" "); if(i==13) i++; printf("%d ",i-13); } printf("\tEXPECT\n\n"); for(j=0;j<20;j++) { printf("%c\t",aminotype[j]); for(i=0;i<15;i++) printf(" %2.0f ",freq[j][i]); printf("\t%4.1f\n",expect[j]); } } for(j=0;j<20;j++) { for(i=0;i<15;i++) { if(freq[j][i]==0) { freq[j][i]=1; if(i==10||i==12) freq[j][i]=expect[j]/SAMPLE; } weight[j][i]=log(freq[j][i]/expect[j]); } } if(argc==1) { printf("\n\nWEIGHT MATRIX (x 100)\n\n"); printf(" "); for(i=0;i<16;i++) { if(i>3) printf(" "); if(i>12) printf(" "); if(i==13) i++; printf(" %d",i-13); } printf("\n\n"); for(j=0;j<20;j++) { printf("%c ",aminotype[j]); for(i=0;i<15;i++) printf("%4.0f ",100*(weight[j][i])); printf("\n"); } printf("\nmethod from: Gunnar von Heijne, NAR 14, p.4683, 1986\n"); } if(argc!=1) { if((fp=fopen(seqfile,"r"))==NULL) printf("no such file\n"); if(argc==2) printf("\n\nSCORE PROFILE of %s\n\ncleave\tscore\tresidue\n\n",seqfile); while((c=getc(fp))!=EOF&&c!=NULL) { if(c==' '||c=='\t'||c=='\n') continue; seqbuff[14]=c; for(i=0;i<15;i++) for(j=0;j<20;j++) if(seqbuff[i]==aminotype[j]) score[k] += weight[j][i]; if(score[k]>max) { max=score[k]; shift=k; } if(k>1) { if(argc>2&&score[k]<0) printf("%d\t0",k-1); else { if(argc>2) printf("%4.2f\t0\n",k-1.25); printf("%d\t%4.2f", k-1, score[k]); if(argc>2) printf("\n%4.2f\t0",k-0.75); } } if(argc==2) printf("\t%c",seqbuff[12]); printf("\n"); for(i=0;i<14;i++) seqbuff[i]=seqbuff[i+1]; k++; } if(argc==2) { printf("\nmax score is %4.2f, cleaved after res %d\n\n",max,shift-1); if(max<0.0) printf("improbable signal sequence\n"); if(max>=0.0&&max<5.0) printf("possible but ambiguous signal\n"); if(max>=5.0&&max<10.0) printf("probable signal sequence\n"); if(max>=10.0) printf("highly probable signal sequence\n"); } else { printf("%d\t0\t\" \"\n",k-1); printf("%d\t%4.2f\t\\n",shift-1,max,shift-1,max); printf("%d\t2.5\tpossible\n",k); printf("%d\t7.5\tprobable\n",k); printf("%d\t12.5\tdefinite\n",k); } } } From owner-proteins@net.bio.net Wed Dec 15 22:00:00 1993 Path: biosci!daresbury!not-for-mail From: "Andrew, Tel. +39-6-91093434" Newsgroups: bionet.molbio.proteins Subject: Possible lead on basic chitinase antibody Date: 16 Dec 1993 08:24:09 -0000 Lines: 15 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2ep5v9$gfs@mserv1.dl.ac.uk> Original-To: proteins@dl.ac.uk In article bionet.molbio.proteins Msg # 775, Nishant (nbhatia@ucdavis.edu) writes: > I'm looking for a basic chitinase antibody which might cross > react with extracellular proteins I am purifying from plant tissue culture > extracts of chinese cucumber. I'd appreciate any information or leads to a > source for the above. One possible source might be the group of Fred Meins at the Friedrich Miescher institute in Basel, Switzerland. His people used to work on basic and acidic chitinases (though in tobacco, I think) and maybe he can provide you with material or contacts. Regards, Andrew Wallace, IRBM P. Angeletti, Pomezia, Italy From owner-proteins@net.bio.net Wed Dec 15 22:00:00 1993 Newsgroups: bionet.general,bionet.molbio.proteins,bionet.molbio.pir,bionet.software,bionet.xtallography,bionet.molbio.methds-reagnts Path: biosci!bcm!cs.utexas.edu!swrinde!gatech!darwin.sura.net!news.gdb.org!dev.gdb.org!danj From: danj@dev.gdb.org (Dan Jacobson) Subject: New Web (WWW) Server for Biology Message-ID: <1993Dec15.195545.2176@news.gdb.org> Sender: news@news.gdb.org Nntp-Posting-Host: dev.gdb.org Organization: The Johns Hopkins University - Genome Data Base (GDB) Date: Wed, 15 Dec 1993 19:55:45 GMT Lines: 34 Xref: biosci bionet.general:6828 bionet.molbio.proteins:1151 bionet.molbio.pir:1 bionet.software:6754 bionet.xtallography:618 bionet.molbio.methds-reagnts:9867 I'm happy to announce the birth of The Johns Hopkins University BioInformatics Web Server - a new