From owner-proteins@net.bio.net Fri Oct 02 23:00:00 1992 Path: biosci!ucselx!sol.ctr.columbia.edu!destroyer!gatech!rutgers!att-out!pacbell.com!iggy.GW.Vitalink.COM!psinntp!psinntp!alsys1!aecom.yu.edu! From: @aecom.yu.edu Newsgroups: bionet.molbio.proteins Subject: Wanted: Good gel analysis software Summary: looking for gel scanning software for PC compatible Keywords: gel Message-ID: <.5@aecom.yu.edu> Date: 1 Oct 92 13:54:46 GMT Sender: news@alsys1.aecom.yu.edu Organization: Albert Einstein College of Medicine Lines: 10 Nntp-Posting-Host: confocal.aecom.yu.edu Does anybody know of good software for analyzing gels that runs on a 486 or 386? We are interested in a comprehensive package. Our current hardware includes a high resolution CCD camera digitized on a PC compatible. Thanks- Michael cammer@aecom.yu.edu From owner-proteins@net.bio.net Mon Oct 05 23:00:00 1992 Path: biosci!SHY.NEURO.UPENN.EDU!GARBERN From: GARBERN@SHY.NEURO.UPENN.EDU ("GARBERN") Newsgroups: bionet.molbio.proteins Subject: Phosphoaminoacids Message-ID: <9210070218.AA04070@net.bio.net> Date: 7 Oct 92 02:19:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 10 Dear networlders, At the risk of sounding stupid: Are there any quick and easy methods for easily distinguishing the different phosphoamino acids, without having to use HPLC, Mass spec or high voltage electrophoresis? For instance, are there any TLC methods? Thanks, Jim Garbern Neurology garbern@shy.neuro.upenn.edu From owner-proteins@net.bio.net Thu Oct 15 23:00:00 1992 Path: biosci!news.cs.indiana.edu!noose.ecn.purdue.edu!mentor.cc.purdue.edu!purdue!gatech!destroyer!caen!uakari.primate.wisc.edu!usenet.coe.montana.edu!news.u.washington.edu!serval!yoda.eecs.wsu.edu!jfletche From: jfletche@yoda.eecs.wsu.edu (Justin Fletcher - CS) Newsgroups: bionet.molbio.proteins,bionet.software Subject: Request: rule base for protein structure prediction Message-ID: <1992Oct16.191743.13358@serval.net.wsu.edu> Date: 16 Oct 92 19:17:43 GMT Sender: news@serval.net.wsu.edu (USENET News System) Organization: Washington State University Lines: 11 Xref: biosci bionet.molbio.proteins:398 bionet.software:3459 I'm hoping to avoid duplicating any work that may have been to convert V.I. Lim's rules for determining the secondary structure for proteins as described in the Journal of Molecular Biology (vol. 88, 1974) to an expert system rule base. If you have or know of such a rule base, your assistance would be greatly appreciated. -- Justin Fletcher Washington State University jfletche@eecs.wsu.edu From owner-proteins@net.bio.net Sun Oct 18 23:00:00 1992 Path: biosci!agate!stanford.edu!rock!concert!duke!news.duke.edu!canctr.mc.duke.edu!RLA From: rla@canctr.mc.duke.edu Newsgroups: bionet.molbio.proteins Subject: looking for DSSP program Message-ID: <6103@news.duke.edu> Date: 18 Oct 92 13:55:09 GMT Sender: news@news.duke.edu Reply-To: rla@canctr.mc.duke.edu Organization: Duke U. Med. Ctr., Durham, NC Lines: 13 Nntp-Posting-Host: canctr.mc.duke.edu Anyone know where I can get a VMS executable of the secondary structure description program DSSP which works on Brookhaven 3D coordinate files? This information is usually incorporated into the headers of pdb files but when it isn't, this program is supposed to be able to generate it. If executable is not available, fortran or C code can be compiled. advTHANKSance Rick Alston Post: Duke University Medical Center rla@canctr.mc.duke.edu Comprehensive Cancer Center Phone: 919.684.6944 Box 3424, DUMC FAX: 919.684.2311 Durham, NC 27710 From owner-proteins@net.bio.net Sun Oct 18 23:00:00 1992 Path: biosci!news.cs.indiana.edu!sgiblab!zaphod.mps.ohio-state.edu!cis.ohio-state.edu!news.sei.cmu.edu!drycas.club.cc.cmu.edu!cantaloupe.srv.cs.cmu.edu!das-news.harvard.edu!husc-news.harvard.edu!husc10!ng4 From: ng4@husc10.harvard.edu (Ho Leung Ng) Newsgroups: bionet.molbio.proteins Subject: text wanted Message-ID: Date: 19 Oct 92 21:09:52 GMT Distribution: usa Lines: 10 Nntp-Posting-Host: husc10.harvard.edu I am looking for a book: Brooks, Karplus, and Pettitt - Proteins: A Theoretical Perspective of Dynamics, Structure & Thermodynamics Thank you. Ho Leung Ng From owner-proteins@net.bio.net Tue Oct 20 23:00:00 1992 Path: biosci!agate!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!zaphod.mps.ohio-state.edu!usc!sol.ctr.columbia.edu!destroyer!cs.ubc.ca!utcsri!newsflash.concordia.ca!nstn.ns.ca!morgan.ucs.mun.ca!kean.ucs.mun.ca!jgill From: jgill@kean.ucs.mun.ca Newsgroups: bionet.molbio.proteins Subject: densitometry Message-ID: <1992Oct21.101504.1@kean.ucs.mun.ca> Date: 21 Oct 92 12:45:04 GMT Sender: usenet@morgan.ucs.mun.ca (NNTP server account) Organization: Memorial University. St.John's Nfld, Canada Lines: 14 To whom it may concern: I was wondering if anyone knows of a software package capable of carrying out densitometry, (ie, on autoradiograms). This package should be IBM compatible and at the same time be able to work with a Hewlett Packard 'ScanJet Plus' scanner. I was looking at a package carried by Fotodyne, however, it is a fairly expensive package. So I was wondering if anyone knows of a cheaper package which is IBM compatible, unlike the Mac compatible package offered by Fotodyne. thanx, Juan From owner-proteins@net.bio.net Tue Oct 20 23:00:00 1992 Path: biosci!agate!spool.mu.edu!uunet!mcsun!sunic!ugle.unit.no!nuug!nntp.uio.no!news From: RODRIGOL@BIOMED.UIO.NO (Rodrigo Lopez) Newsgroups: bionet.molbio.proteins Subject: Re: looking for DSSP program Message-ID: <1992Oct21.102748.2969@ulrik.uio.no> Date: 21 Oct 92 10:27:48 GMT References: <6103@news.duke.edu> Sender: news@ulrik.uio.no (Mr News) Organization: THe Norwegian EMBnet node Lines: 22 In-Reply-To: rla@canctr.mc.duke.edu's message of 18 Oct 92 13:55:09 GMT Nntp-Posting-Host: biomed.uio.no X-News-Reader: VMS NEWS 1.24 In <6103@news.duke.edu> rla@canctr.mc.duke.edu writes: > Anyone know where I can get a VMS executable of the secondary structure > description program DSSP which works on Brookhaven 3D coordinate files? This > information is usually incorporated into the headers of pdb files but when it > isn't, this program is supposed to be able to generate it. > > If executable is not available, fortran or C code can be compiled. > > advTHANKSance > > Rick Alston Post: Duke University Medical Center > rla@canctr.mc.duke.edu Comprehensive Cancer Center > Phone: 919.684.6944 Box 3424, DUMC > FAX: 919.684.2311 Durham, NC 27710 Contact Dr. Chris Sander at The EMBL (European Molecular Biology Lab) in Heidelberg. e-mail: sander@embl-heidelberg.de R:-) From owner-proteins@net.bio.net Tue Oct 20 23:00:00 1992 Path: biosci!NBRF.GEORGETOWN.EDU!POSTMASTER From: POSTMASTER@NBRF.GEORGETOWN.EDU Newsgroups: bionet.molbio.proteins Subject: Re: PIR vs PDB: Crossref? Sequence corrections? Message-ID: <01GQ7U1PR0AQ8WW70W@NBRF.Georgetown.Edu> Date: 21 Oct 92 22:19:17 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 67 Michael Weise asking about PIR cross-references to PDB presented an analysis that puts the problem very clearly --- a sequence in Brookhaven is not necessarily the same as the sequences in PIR for what should supposedly be the same protein. (If you look at the SWISS-PROT cross-refs I think you will very quickly see that the cross-referenced sequences are also not identical for many of the entries.) Michael looked at the first NRL_3D entry, noticed this problem and asked how bad it was. I can assure you, it is bad. Within the last few years the staff at Brookhaven began checking newly submitted sequences against the PIR and trying to resolve discrepancies before publication. This has helped but does not clear up the problem for entries submitted prior to the adoption of that check procedure. At our end of the process we felt that a more comprehensive approach was called for. Construction of the NRL_3D database was the first step in preparing the cross-references to Brookhaven for PIR. Beginning with Release 10.00 of NRL_3D, the Brookhaven Protein Dank Bank will not be completely converted with each release. Instead only new or revised entries in the PDB will be converted and merged with NRL_3D. Entries in NRL_3D will now be subjected to the same checking, annotation and revision process as the other PIR databases. This will allow us to standardize (and occasionally correct) the protein names, the enzyme names and numbers, the species names and the features appearing in the NRL_3D. We have begun an entry-by-entry evaluation of NRL_3D, as part of which the appropriate cross-references and sequence specification records (detailing all sequence differences) will be generated. We hope that these cross-references will begin appearing in PIR entries in the near future. (There are still a few bugs to be worked out.) When they appear it should be possible to use the ATLAS program and the PIR Network Request Server to generate a list of PIR entries containing PDB cross-references. We may also provide a list of those cross-references retrievable from the Network Server. Michael commented that the codes in the NRL_3D are the same as in the PDB. That is not quite correct. The first four characters of the codes are always the same. After release 9.1 of NRL_3D, an alphabetic character following those first four denotes a separate peptide chain in the PDB entry. Numeric characters following those first four, and the chain character if there is one, denote a fragment number. The chain characters are the same as the chain ID's in the PDB whenever possible but chain ID numbers are converted to the corresponding alphabetic characters. The fragment numbers are assigned in the order they are detected, but some are discarded if they contain fewer than three recognizable residues. Michael also asked, > (Also, shouldn't there be some effort to update/correct PDB sequence data?) You should remember that the experimenter uses a specific sequence in the refinement process and it is that sequence that becomes the "experimental data" in the represented 3-D structure. You could not and should not simply go back and make changes in the sequence and assume that the same 3-D structure would have been generated. Granted, most people would do that as a first approximation, but then it should not be up to us at the databases to make those experimental assumptions. Members of the staff at both Brookhaven and the PIR are engaged in this effort. We feel that our objectives should be both to find the correct cross-references and to report the sequence differences in the way that is most scientifically valid and reliable. I hope I have answered your questions. ------------------------------------------------------------------------ Dr. John S. Garavelli Database Coordinator Protein Identification Resource National Biomedical Research Foundation Washington, DC 20007 POSTMASTER@GUNBRF.BITNET POSTMASTER@NBRF.GEORGETOWN.EDU From owner-proteins@net.bio.net Tue Oct 20 23:00:00 1992 Path: biosci!uwm.edu!wupost!crcnis1.unl.edu!moe.ksu.ksu.edu!zaphod.mps.ohio-state.edu!sol.ctr.columbia.edu!spool.mu.edu!nigel.msen.com!emory!athena.cs.uga.edu!news From: WEISE@bscf.uga.edu (MICHAEL WEISE) Newsgroups: bionet.molbio.proteins Subject: PIR vs PDB: Crossref? Sequence corrections? Message-ID: <1992Oct21.162925.8603@athena.cs.uga.edu> Date: 21 Oct 92 16:29:25 GMT Sender: news@athena.cs.uga.edu Organization: University of Georgia, USA Lines: 54 X-News-Reader: VMS NEWS 1.20 The distribution for the Swiss-Prot database has a file which lists all SP entries with pointers to Brookhaven PDB. Does a similar list exist for PIR database entries? Why the interest in such lists? Well, lists w/ PDB pointers are useful in creating 'indirect' files that allow the FastDB (IG Suite) and the FastA (GCG package) programs to search only entries in Swiss-Prot or PIR that have references to PDB. Admittedly, the NRL_3D database is available and can easily be setup for use with GCG's FastA, so one might assume the indirect file approach is semi-redundant (unless you're interested in using IG's program, in which case a NRL_3D setup isn't possible). However, in looking at NRL_3D you find that the database has been generated by creating .SEQ and .REF files from PDB directly. This unfortunately gives a database where entries are identified by PDB ID's (instead of PIR Codes) and for which there apparently isn't a check on whether sequences have been updated/corrected compared to corresponding PIR entries. (I've looked at the first NRL_3D entry < 155c > which should correlate with PIR's CCPC50. The two are aligned below. While they are largely the same, note that they are NOT identical. 10 20 30 40 50 155c NEGDAAKGEKEFNKCKACHMIQAPDGTD-IKGGKTGPNLYGVVGRKIASEEGFKYGEGIL ::|||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| Ccpc50 QDGDAAKGEKEFNKCKACHMIQAPDGTDIIKGGKTGPNLYGVVGRKIASEEGFKYGEGIL 10 20 30 40 50 60 60 70 80 90 100 110 155c EVAEKNPDLTWTEANLIEYVTDPKPLVKKMTDDKGAKTKMTFKMGKNQADVVAFLAQDDP ||||||||||||||:|||||||||| : |||||||||||||||||||||||||||||::| Ccpc50 EVAEKNPDLTWTEADLIEYVTDPKPWLVKMTDDKGAKTKMTFKMGKNQADVVAFLAQNSP 70 80 90 100 110 120 120 130 155c DAXXXXXXXXXXXXX || Ccpc50 DAGGDGEAA I haven't looked to see if there are other examples of sequence differences, but I'd be happy if someone either could tell me there aren't any more or could give some idea of how widespread the problem is.) So, it would appear that there may be additional utility in having PIR/PDB crossreference list. It would provide an easy way of checking if changes have been made to the sequence from when it was originally added to the PDB. Thus, if a PIRtoPDB list doesn't yet exist, what would it take to generate one and make it a permanent part of the PIR distribution? (Also, shouldn't there be some effort to update/correct PDB sequence data?) MJW _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ / Michael J. Weise, Ph.D. \ Univ.of Ga. BioScience Computing Facility \ ( weise@bscf.uga.edu \ Dept.of Genetics UGa, Athens GA 30602 ) \ _ _ _'Tis_only_me_speak'n._ _\_ _ _ _ _ _ _ (706) 542-1409_ _ _ _ _ _ _ / From owner-proteins@net.bio.net Sun Oct 25 22:00:00 1992 Path: biosci!mis.mcw.edu!FGARBRECHT From: FGARBRECHT@mis.mcw.edu Newsgroups: bionet.molbio.proteins Subject: Western blot re-probing Message-ID: <01GQEJ63CA2A8WW2I5@mis.mcw.edu> Date: 26 Oct 92 17:47:32 GMT Sender: daemon@net.bio.net Distribution: bionet Organization: Medical College of Wisconsin (Milwaukee, WI) Lines: 5 Is it possible to strip and re-probe a Western blot? Has anyone a method or a reference? Thanks Fred Garbrecht Medical College of Wisconsin From owner-proteins@net.bio.net Tue Oct 27 22:00:00 1992 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!darwin.sura.net!paladin.american.edu!news.univie.ac.at!hp4at!mcsun!uknet!comlab.ox.ac.uk!oxuniv!oxpath!rpgrant From: rpgrant@vax.path.ox.ac.uk Newsgroups: bionet.molbio.proteins Subject: Re: Western blot re-probing addendum Message-ID: <1992Oct28.103857.1@vax.path.ox.ac.uk> Date: 28 Oct 92 09:38:57 GMT References: <01GQEJ63CA2A8WW2I5@mis.mcw.edu> Distribution: bionet Organization: Oxford University Molecular Biology Data Centre Lines: 3 Nntp-Posting-Host: heatly Nntp-Posting-User: rpgrant PS In step one of the protocol I gave, agitate the filters occasionally (tell them you're going to use 125-iodine - yuk!) Richard From owner-proteins@net.bio.net Tue Oct 27 22:00:00 1992 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!darwin.sura.net!paladin.american.edu!news.univie.ac.at!hp4at!mcsun!uknet!comlab.ox.ac.uk!oxuniv!oxpath!rpgrant From: rpgrant@vax.path.ox.ac.uk Newsgroups: bionet.molbio.proteins Subject: Re: Western blot re-probing Message-ID: <1992Oct28.100139.1@vax.path.ox.ac.uk> Date: 28 Oct 92 09:01:39 GMT References: <01GQEJ63CA2A8WW2I5@mis.mcw.edu> Distribution: bionet Organization: Oxford University Molecular Biology Data Centre Lines: 35 Nntp-Posting-Host: heatly Nntp-Posting-User: rpgrant In article <01GQEJ63CA2A8WW2I5@mis.mcw.edu>, FGARBRECHT@mis.mcw.edu writes: > Is it possible to strip and re-probe a Western blot? Has anyone > a method or a reference? Thanks It _is_ possible, with limited success. I use the ECL system from Amersham, and the following protocol for stripping and re-probing (which is slightly modified from that given by them): 1. Incubate filters in 2% SDS, 62.5mM Tris-Cl pH 6.8, 100mM 2-mercaptoethanol at 50C for 30 min. Remove filters into fresh buffer and incubate for a further 30 min. The buffer should be pre-warmed. I make it up from a 5X stock and add 2-ME fresh each time. I usually strip 2 6x8cm filters in 50ml buffer in 50ml Falcon tubes with the lid sealed with parafilm. 2. Wash filters in 500ml (yes, 500) PBS/0.1% Tween 20 at RT for 10min, twice. 3. Block in milk powder (or whatever), wash well and probe as normal. I find this protocol removes (guesstimate) 90% of the signal. It's not perfect, but I find it adequate if I play with the exposure times. Standard disclaimer: I have nothing whatever to do with Amersham, except for using their products occasionally. > Fred Garbrecht > Medical College of Wisconsin Richard Grant Oxford University From owner-proteins@net.bio.net Wed Oct 28 22:00:00 1992 Path: biosci!agate!ames!saimiri.primate.wisc.edu!mimbres.cs.unm.edu!unmvax!cs.sandia.gov!twarnow From: twarnow@cs.sandia.gov (Tandy Warnow) Newsgroups: bionet.molbio.proteins Subject: Molecular Sequence Alignment Tutorial and Workshop Summary: Nov. 5-6, 1992, at the Univ. of New Mexico Message-ID: <1992Oct29.190138.24419@cs.sandia.gov> Date: 29 Oct 92 19:01:38 GMT Sender: usenet@cs.sandia.gov (Another name for news) Distribution: bionet Organization: Sandia National Laboratories, Albuquerque, NM Lines: 224 Tutorial and Workshop on Algorithms for Molecular Sequence Alignment Nov. 5 - 6, 1992 University of New Mexico, Albuquerque, NM Sandia National Laboratories and the Computer Science Department at the University of New Mexico are pleased to announce a tutorial and workshop on {\em Algorithms for Molecular Sequence Alignment}, to be held on Nov. 5 and 6, 1992, at the University of New Mexico, in Albuquerque, NM. The tutorial is designed to introduce the problem of molecular sequence alignment, while the workshop will focus on new algorithmic techniques for this fundamental problem in computational biology. Note that no background in biology is assumed for the tutorial! The tutorial and workshop will be free and open to the public. Graduate students and postdocs are especially encouraged to attend. For further information about this workshop and tutorial, please contact Tandy Warnow at (505) 845-7604, or send email to twarnow@cs.sandia.gov. This workshop and tutorial immediately precedes the meeting of the Program in Mathematics and Molecular Biology on "Nucleic Acids: Structure and Function", to be held from Nov. 7-11, in Santa Fe, NM. For further information about the PMMB meeting, please contact Sylvia Spenger, at (510) 643-7799, or send email to sylviaj@violet.berkeley.edu. Although we do not require registration, we would appreciate knowing if you plan on attending, so that we can make local arrangements. Therefore, please send email to twarnow@cs.sandia.gov to let us know of your intent. Thank you! Thursday, Nov. 5: Tutorial 9:00-4:00, The Cellar, Hokona Hall, University of New Mexico Topics to be covered include: biological background, optimal pairwise alignments, global and local alignment, suboptimal pairwise alignments, distance vs. similarity, scoring matrices, database searching, and multiple alignment: trees and profiles. Instructor: Martin Vingron Department of Mathematics University of Southern California Friday, Nov. 6: Workshop 9:00-4:00, The Cellar, Hokona Hall, University of New Mexico Lectures: "On Suboptimal Alignments of Biological Sequences" Dalit Naor Department of Biochemistry Stanford University "Multiple Alignment with Guaranteed Error Bounds" Pavel Pevzner Department of Computer Science Pennsylvania State University "Scoring Systems for Macromolecular Sequence Comparison" Stephen Altschul National Institute of Health "The Maximum Weight Multiple Sequence Trace Problem" John Kececioglu Department of Computer Science University of California at Davis "Analysis and Biological Evaluation of Parametric Sequence Alignments" Martin Vingron Department of Mathematics University of Southern California "Dinucleotide Simple Sequence Repeats in Human DNA" David Torney Los Alamos National Laboratories "3-D Profile Method and its Application in Protein Secondary Structure Prediction" Kam Zhang Molecular Biology Institute University of California at Los Angeles Local information regarding the Workshop and Tutorial on ALGORITHMS FOR MOLECULAR SEQUENCE ALIGNMENT Dear Friends and Colleagues, Enclosed is some detailed information about the workshop and tutorial on Algorithms for Molecular Sequence Alignment. Although no registration is required and the workshop and tutorial are free and open to the public, we would appreciate knowing that you are planning on attending so that we can make further arrangements (i.e. food, van transportation to the workshop, etc.). In particular, you should let us know what hotel you'll be staying at, as we will leave materials at these hotels for you when you register. Since some people have asked, the tutorial will cover everything you need to know in order to follow the research talks at the workshop. No background is required! We look forward to seeing you! Dates: Tutorial: Nov 5, 1992, 9:00-4:00 Workshop: Nov. 6, 1992, 9:00-4:00 Location: The Cellar, Hokona Hall University of New Mexico (on the south side of Las Lomas Road -- aka Campus Blvd) Parking: Opposite Hokona Hall, in the Parking Structure between Lomas Blvd. and Las Lomas Road. IF YOU WILL BE PARKING ON CAMPUS, YOU MUST LET US KNOW SO WE CAN ARRANGE FOR A PERMIT FOR YOU! (Parking on campus is difficult at best, so it is recommended that you walk or use the van service provided by the Raddison Hotel instead.) Time: Please plan on being at the workshop and tutorial by 8:45 AM each day, as we will begin by 9:00 SHARP. We will have a 2 hour lunch break each day from 12:00-2:00, and finish by 4:30 PM. Refreshments: We will be providing refreshments at breakfast and during the breaks. Therefore, please let us know that you will be attending, so we can order enough food and coffee! The best way to do this is by email. You will now find a list of hotels for accomodations during your stay in Albuquerque. We have reserved a block of 30 rooms at the Raddison Inn at a special government rate. This hotel will provide van transportation to the campus in the morning and back again in the evening, so that it won't be necessary to rent a car. Raddison Inn Albuquerque 1-(800)333-3333 or (505) 247-0512, 1901 Univ. SE $53.00 plus tax single, mention "Sandia National Labs" when calling to obtain this government rate. 30 rooms available, checking in on 4th of Nov., checking out on 5th complementary use of Midtown Athletic Club; hotel van will provide free transportation to the club. Heated pool, whirlpool, airport transportation Hotel will provide transportation by van to the workshop in the morning and back in the evening. Alternate Hotels: Plaza Inn Albuquerque (2 Star, AAA) 900 Medical Arts NE (505) 243-5693 swimming pool may be close enough to walk to the workshop and tutorial $55.00 plus tax Albuquerque Hilton (3 Star, AAA) 1901 University Blvd. NE 1-800-HILTONS heated pools, sauna, tennis $79.00 Albuquerque Marriott (4 Star, AAA) 2101 Louisiana 1-(505)881-6800 heated pool, sauna, whirpool, airport transportation $114.00 plus tax Barcelona Court (3 Star, AAA) 900 Louisiana Blvd. NE 1-(505) 255-5566 all suites, free breakfast, heated pools, sauna, whirpool single $74.95, 2 adults plus up to 2 children $84.95 (plus tax) University Lodge (2 Star, AAA) 3711 Central Ave, NE 1(505) 266-7663 One block from the "Nob Hill" area at Central and Carlisle. Great area for cafes and bookstores, but supposed to be not a good place for hotels (unsavory clientelle is the complaint). I have no personal experience with this hotel, and suggest it only if you want to keep the price down. You can walk from here to the workshop and tutorial. $16.95 There are many excellent restaurants in town, and several fun cafes and bookstores. If you choose to rent a car, be warned that parking will be difficult at the campus. We will try to arrange parking, but please try to arrive by 8:30 to find parking, in order to be at the workshop or tutorial by 9, as it can take time even with a permit to find a space. It may be easier to NOT rent a car, and use the van (from the Raddison) or else stay somewhere reasonably close and walk. Please do let me know if you're coming and where you'll be staying, as I will try to arrange to get maps to you. For further information, please contact Tandy Warnow at twarnow@cs.sandia.gov. From owner-proteins@net.bio.net Sat Oct 31 22:00:00 1992 Path: biosci!agate!ames!haven.umd.edu!uunet!utcsri!torn!newshost.uwo.ca!uwovax.uwo.ca!37_1510 From: 37_1510@uwovax.uwo.ca Newsgroups: bionet.molbio.proteins Subject: Re: Genetics transposons conventions... Message-ID: <1992Nov1.211151.1@uwovax.uwo.ca> Date: 2 Nov 92 01:11:51 GMT References: Sender: news@julian.uwo.ca (USENET News System) Organization: University of Western Ont, London Lines: 29 Nntp-Posting-Host: hydra.uwo.ca In article , wbrown@access.digex.com (William Brown) writes: > I hope somebody can help me with this problem. My research is in > modeling, so I've gotten a little rusty on the genetics end of things. > I'm reading a paper that includes the following descriptions of > transposons in its PROCEDURES section, and for the life of me I don't know > what they are talking about: Hfr::Tn10, zcf::Tn10, and srl::Tn10. I KNOW > what Tn10 is - a P1 phage-transfer unstable transposon carrying > tetracycline resistance. I HAVE NO IDEA what the meanings of the > three-letter prefixes are. Could anyone out there clear this up for me? > I've browsed through dozens of references to no avail, and I will not be > in the office anytime soon to ask someone in person. I'd greatly > appreciate some clarification. This is very frustrating. > > William Brown > The three letter symbols correspond to the gene where the transposon is inserted. ie. srl=sorbitol. Hfr means an F plasmid integrated in the chromosome that is capable of initiating the transfer of chromosomal infomrmation by conjugation. In this case, Hfr::Tn10 means the the transposon is inserted in the integrated F sequences. the nomeclature based on z?? means that the transposon is inserted in specific regiomns of the chromosomal map (arbitrarily fragmented in minutes) but the gene with the insertion is not known as yet. The precise explanation for the latter is in a paper published on the journal Genetics by John Roth and coll, I beilive in the 80', but I do not have the reference available right now. If don't find it please drop me a message, and I will get it for you. Good luck. Miguel A. Valvano. Microbiology and Immunology, University of Western Ontario, London, Ontario.