From owner-gcg@net.bio.net Tue Nov 01 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!gatech!udel!news.sprintlink.net!EU.net!uknet!comlab.ox.ac.uk!oxuniv!oxpath!birney Newsgroups: bionet.software.gcg Subject: SQLoad... Reading Comments???? Message-ID: <1994Nov2.141806.1@ania.path.ox.ac.uk> From: birney@molbiol.ox.ac.uk Date: 2 Nov 94 14:18:06 GMT Organization: Oxford University Molecular Biology Data Centre Nntp-Posting-Host: ania.path.ox.ac.uk Lines: 30 Hi.... I'm trying to use GCG8 calls (in C programs) and I can read sequence fine: BUT I can't seem to get out the comment lot: whne i do FileHandle fileh; struct Sequence SQ; CommentTable table; int position[1024]; DBOpenF(&fileh,seqnamecall); SQLoad(fileh,&SQ,table,position); there seems to be *nothing* in table or position.... Any hints? thanks ewan birney@molbiol.ox.ac.uk From owner-gcg@net.bio.net Tue Nov 01 22:00:00 1994 Path: biosci!rutgers!gatech!udel!news.sprintlink.net!EU.net!uunet!heifetz.msen.com!emory!usenet From: bcresas@bimcore.emory.edu (Scott Sammons) Newsgroups: bionet.software.gcg,bionet.software,bionet.molbio.embldatabank Subject: E. coli Database Collection --> GCG format Date: 2 Nov 1994 20:28:59 GMT Organization: Biomolecular Computing Resource, Emory University Lines: 16 Distribution: world Message-ID: <398sqb$79b@emory.mathcs.emory.edu> Reply-To: bcresas@bimcore.emory.edu NNTP-Posting-Host: bimcore.cc.emory.edu Xref: biosci bionet.software.gcg:801 bionet.software:9889 bionet.molbio.embldatabank:384 Greetings: Has anyone successfully reformatted the ECD data into GCG formatted databases. The program embltogcg core dumps when I try it with one of the ECD .dat files. Scott Sammons ======================================================================= | Scott A. Sammons (404) 727-2780 | | Emory University FAX: (404) 727-3659 | | Biomolecular Computing Resource | | 3025 Rollins Research Center Email: sammons@bimcore.emory.edu | | Atlanta, GA 30322 | ======================================================================= From owner-gcg@net.bio.net Wed Nov 02 22:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!nntp-serv.cam.ac.uk!pmr From: pmr@staffa.sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.gcg,bionet.software,bionet.molbio.embldatabank Subject: Re: E. coli Database Collection --> GCG format Date: 03 Nov 1994 09:45:14 GMT Organization: University of Cambridge, England Lines: 24 Distribution: world Message-ID: References: <398sqb$79b@emory.mathcs.emory.edu> NNTP-Posting-Host: staffa.sanger.ac.uk In-reply-to: bcresas@bimcore.emory.edu's message of 2 Nov 1994 20:28:59 GMT Xref: biosci bionet.software.gcg:802 bionet.software:9901 bionet.molbio.embldatabank:385 In article <398sqb$79b@emory.mathcs.emory.edu> bcresas@bimcore.emory.edu (Scott Sammons) writes: > Has anyone successfully reformatted the ECD data into GCG formatted databases. > The program embltogcg core dumps when I try it with one of the ECD .dat > files. As I am involved in both ECD and EGCG, I will try to put something into EGCG 8.0 when it is ready. I take it you are referring to the very latest (new format) ECD here. Do you mean the genorf.dat file or the contigs/*.dna files (which are closer to EMBL format and have more sequence data)? Beware though - E.coli sequencing is now going so well that ECD has a contig (and more to follow) over the 350k mark, which will give some problems with GCG. Another option would be to use a script (or Perl) to reformat into enough of an "EMBL" format for EMBLtoGCG to accept it. -- ------------------------------------------------------------------------ Peter Rice | Informatics Division E-mail: pmr@sanger.ac.uk | The Sanger Centre Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, Fax: (44) 1223 494919 | Cambs, CB10 1RQ URL: http://www.sanger.ac.uk/~pmr | England From owner-gcg@net.bio.net Wed Nov 02 22:00:00 1994 Path: biosci!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!cea.fr!usenet From: cisitm@albert.cad.cea.fr (Pierre Didierjean) Newsgroups: bionet.software.gcg Subject: *** Q: WHAT KIND OF PEOPLE ON THE NET ? Date: 3 Nov 1994 16:17:37 GMT Organization: SSII Lines: 28 Sender: cisitm@albert.cad.cea.fr Message-ID: <39b2f1$9qn@anemone.saclay.cea.fr> NNTP-Posting-Host: nyassa.cad.cea.fr I'd like to know what kind of people i find on the net. Students, Commercials, Adminitrations, Scientifics or what ?? Is anybody knows that or have statistical results ? What are YOU doing in life ? I am a system administrator. Thanks for the answers and sorry for my english ..... Bye +-----------------------------------------------------------------------------+ | Pierre DIDIERJEAN | | | | Administrateur Systeme UNIX | | Cisi, Aix-en-Provence | | France | +-----------------------------------------------------------------------------+ | email : cisitm@albert.cad.cea.fr | +-----------------------------------------------------------------------------+ From owner-gcg@net.bio.net Wed Nov 02 22:00:00 1994 Path: biosci!agate!darkstar.UCSC.EDU!pellinore!rafael From: rafael@cse.ucsc.edu (David Konerding) Newsgroups: bionet.software.gcg,bionet.software,bionet.molbio.embldatabank Subject: Re: E. coli Database Collection --> GCG format Followup-To: bionet.software.gcg,bionet.software,bionet.molbio.embldatabank Date: 3 Nov 1994 21:14:47 GMT Organization: UC Santa Cruz CIS/CE Lines: 38 Distribution: world Message-ID: <39bjs7$t3p@darkstar.UCSC.EDU> References: <398sqb$79b@emory.mathcs.emory.edu> NNTP-Posting-Host: pellinore.cse.ucsc.edu X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.software.gcg:805 bionet.software:9916 bionet.molbio.embldatabank:387 Peter Rice (pmr@staffa.sanger.ac.uk) wrote: : In article <398sqb$79b@emory.mathcs.emory.edu> bcresas@bimcore.emory.edu (Scott Sammons) writes: : > Has anyone successfully reformatted the ECD data into GCG formatted databases. : > The program embltogcg core dumps when I try it with one of the ECD .dat : > files. : As I am involved in both ECD and EGCG, I will try to put something into EGCG 8.0 : when it is ready. I take it you are referring to the very latest (new format) : ECD here. Do you mean the genorf.dat file or the contigs/*.dna files (which are : closer to EMBL format and have more sequence data)? : Beware though - E.coli sequencing is now going so well that ECD has a contig (and : more to follow) over the 350k mark, which will give some problems with GCG. : Another option would be to use a script (or Perl) to reformat into enough of an : "EMBL" format for EMBLtoGCG to accept it. Hmm. Can anybody give me a pointer to where I can find the ECD? I am writing a thesis which regards computational methods for finding genes in prokaryotic DNA, and any database more complete than EcoSeq6 would be great. Thanks. : -- : ------------------------------------------------------------------------ : Peter Rice | Informatics Division : E-mail: pmr@sanger.ac.uk | The Sanger Centre : Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, : Fax: (44) 1223 494919 | Cambs, CB10 1RQ : URL: http://www.sanger.ac.uk/~pmr | England -- -- O~_ ------------- David Konerding (University of California, Santa Cruz) c/ /' ------- rafael@cse.ucsc.edu ( ) \( ) --- rafael@cats.ucsc.edu From owner-gcg@net.bio.net Wed Nov 02 22:00:00 1994 Newsgroups: bionet.software.gcg,bionet.software,bionet.molbio.embldatabank Path: biosci!rutgers!gatech!howland.reston.ans.net!news.sprintlink.net!EU.net!sun4nl!sci.kun.nl!jackl From: jackl@sci.kun.nl (Jack Leunissen) Subject: Re: E. coli Database Collection --> GCG format Message-ID: Sender: news@sci.kun.nl (News owner) Nntp-Posting-Host: wn2.sci.kun.nl Organization: University of Nijmegen, The Netherlands References: <398sqb$79b@emory.mathcs.emory.edu> Date: Thu, 3 Nov 1994 21:57:55 GMT Lines: 17 Xref: biosci bionet.software.gcg:807 bionet.software:9921 bionet.molbio.embldatabank:389 In <398sqb$79b@emory.mathcs.emory.edu> bcresas@bimcore.emory.edu (Scott Sammons) writes: >Has anyone successfully reformatted the ECD data into GCG formatted databases. >The program embltogcg core dumps when I try it with one of the ECD .dat >files. You might try my program "embl2nbrf", which reformats EMBL-formatted data into NBRF (=PIR) format. GCG handles this, provided you change the format identifier in the .header file from GCG into NBRF. You can find the program at "ftp.caos.kun.nl", via anonymous FTP, in the directory "pub/molbio/embl2nbrf". Best regards, Jack Leunissen CAOS/CAMM Center From owner-gcg@net.bio.net Wed Nov 02 22:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!nntp-serv.cam.ac.uk!pmr From: pmr@staffa.sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.gcg,bionet.software,bionet.molbio.embldatabank Subject: Re: E. coli Database Collection --> GCG format Followup-To: bionet.software.gcg,bionet.software,bionet.molbio.embldatabank Date: 03 Nov 1994 22:44:38 GMT Organization: University of Cambridge, England Lines: 29 Distribution: world Message-ID: References: <398sqb$79b@emory.mathcs.emory.edu> <39bjs7$t3p@darkstar.UCSC.EDU> NNTP-Posting-Host: staffa.sanger.ac.uk In-reply-to: rafael@cse.ucsc.edu's message of 3 Nov 1994 21:14:47 GMT Xref: biosci bionet.software.gcg:806 bionet.software:9918 bionet.molbio.embldatabank:388 In article <39bjs7$t3p@darkstar.UCSC.EDU> rafael@cse.ucsc.edu (David Konerding) writes: > Peter Rice (pmr@staffa.sanger.ac.uk) wrote: > : In article <398sqb$79b@emory.mathcs.emory.edu> bcresas@bimcore.emory.edu (Scott Sammons) writes: > : > Has anyone successfully reformatted the ECD data into GCG formatted databases. > : > The program embltogcg core dumps when I try it with one of the ECD .dat > : > files. > > : As I am involved in both ECD and EGCG, I will try to put something into EGCG 8.0 > : when it is ready. I take it you are referring to the very latest (new format) > : ECD here. Do you mean the genorf.dat file or the contigs/*.dna files (which are > : closer to EMBL format and have more sequence data)? > > Hmm. Can anybody give me a pointer to where I can find the ECD? I am writing > a thesis which regards computational methods for finding genes in prokaryotic > DNA, and any database more complete than EcoSeq6 would be great. The latest ECD is available from ftp.ebi.ac.uk in directory pub/databases/ecdc (note the extra c at the end :-) The new format is described in: Kroeger et al. (1994); Nucleic Acids Research 22:3450-3455. The contigs directory has the non-redundant contiguous sequences from E.coli K-12. -- ------------------------------------------------------------------------ Peter Rice | Informatics Division E-mail: pmr@sanger.ac.uk | The Sanger Centre Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, Fax: (44) 1223 494919 | Cambs, CB10 1RQ URL: http://www.sanger.ac.uk/~pmr | England From owner-gcg@net.bio.net Wed Nov 02 22:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!sunsite.doc.ic.ac.uk!charlie.lif.icnet.uk!morpheus.lif.icnet.uk!user From: mike@bison.lif.icnet.uk (Mike Mitchell) Newsgroups: bionet.software.gcg Subject: Re: *** Q: WHAT KIND OF PEOPLE ON THE NET ? Date: Thu, 03 Nov 1994 20:16:59 +0100 Organization: Imperial Cancer Research Fund Lines: 52 Message-ID: References: <39b2f1$9qn@anemone.saclay.cea.fr> NNTP-Posting-Host: morpheus.lif.icnet.uk In article <39b2f1$9qn@anemone.saclay.cea.fr>, cisitm@albert.cad.cea.fr (Pierre Didierjean) wrote: > I'd like to know what kind of people i find on the net. > > Students, Commercials, Adminitrations, Scientifics or what ?? > > Is anybody knows that or have statistical results ? > > > What are YOU doing in life ? > > I am a system administrator. > > > Thanks for the answers and sorry for my english ..... > > > > Bye > > > +-----------------------------------------------------------------------------+ > | Pierre DIDIERJEAN | > | | > | Administrateur Systeme UNIX | > | Cisi, Aix-en-Provence | > | France | > +-----------------------------------------------------------------------------+ > | email : cisitm@albert.cad.cea.fr | > +-----------------------------------------------------------------------------+ The sort of people who post a stupid message to every newsgroup available! -- * ***************************************************************** * *Michael Mitchell *"All I know about babies is that you * *User Support * are not supposed to put them into * *Molecular Biology Software * washing machines. Makes the colours * *Imperial Cancer Research Fund* run, presumably." * *+44 (0)71 269 3115 * Tom Holt - Here Comes The Sun - 1994* * ***************************************************************** * From owner-gcg@net.bio.net Thu Nov 03 22:00:00 1994 Path: biosci!MOLBIO.CBS.UMN.EDU!jknott From: jknott@MOLBIO.CBS.UMN.EDU (Julie Knott) Newsgroups: bionet.software.gcg Subject: Re: *** Q: WHAT KIND OF PEOPLE ON THE NET ? Date: 3 Nov 1994 16:17:08 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net On Thu, 3 Nov 1994, Mike Mitchell wrote: > In article <39b2f1$9qn@anemone.saclay.cea.fr>, cisitm@albert.cad.cea.fr > (Pierre Didierjean) wrote: > > > I'd like to know what kind of people i find on the net. > > > > Students, Commercials, Adminitrations, Scientifics or what ?? > > > > Is anybody knows that or have statistical results ? > > > > > > What are YOU doing in life ? > > *****I am a GCG user -- a technician in a molecular biology laboratory***** From owner-gcg@net.bio.net Thu Nov 03 22:00:00 1994 Path: biosci!MCRCR6.MED.NYU.EDU!HILLJ01 From: HILLJ01@MCRCR6.MED.NYU.EDU (John Edward Hill) Newsgroups: bionet.software.gcg Subject: Re: AA 3 letter to 1 letter code Date: 4 Nov 1994 05:46:14 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 39 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <1994Nov4.131358.11868@rzu-news.unizh.ch> NNTP-Posting-Host: net.bio.net The REFORMAT command in GCG has the following option: /THReeintoone translates three-letter peptides into one-letter That should do it! Best, John ___________________________________________________________________________ John Edward Hill, Ph.D. | Department of Cell Biology Internet: hillj01@mcrcr.med.nyu.edu | New York University Medical Center EARN/Bitnet: HILL@NYUMED.BITNET | 550 First Avenue 212-263-7135 FAX: 212-263-8139 | New York, New York 10016 ___________________________________________________________________________ On Fri, 4 Nov 1994, Christoph Weber wrote: > Hi all, > > I have to pull out sequences from PDB files and get them into GCG format. > > In the PDB files the three letter code is used, while GCG only accepts > one letter codes. > I poked around in the help files for a utility to translate between the > two representations, but haven't found anything. > In NBRL3D, I found about half of my sequences and successfully downloaded them > in a GCG readable format, but it's the ones not in NBRL3D (yet) that bug me. > > Does anyone out there know how to go about this? > > Thanks in advance, > Christoph > -- > Christoph Weber email: cweber@oci.unizh.ch > OCI Uni Zurich phone: +41 1 257 4925 > Winterthurerstr. 190 FAX: +41 1 361 9895 > CH-8057 Zurich, Switzerland > > From owner-gcg@net.bio.net Thu Nov 03 22:00:00 1994 Newsgroups: bionet.software.gcg Path: biosci!agate!howland.reston.ans.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!rzusuntk.unizh.ch!cweber From: cweber@oci.unizh.ch (Christoph Weber) Subject: AA 3 letter to 1 letter code Message-ID: <1994Nov4.131358.11868@rzu-news.unizh.ch> Summary: PDB SEQRES to GCG sequence reformatting? Sender: newsadm@rzu-news.unizh.ch (CNEWS ADMINISTRATION) Organization: University of Zurich, Switzerland X-Newsreader: TIN [version 1.2 PL2] Date: Fri, 4 Nov 1994 13:13:58 GMT Lines: 20 Hi all, I have to pull out sequences from PDB files and get them into GCG format. In the PDB files the three letter code is used, while GCG only accepts one letter codes. I poked around in the help files for a utility to translate between the two representations, but haven't found anything. In NBRL3D, I found about half of my sequences and successfully downloaded them in a GCG readable format, but it's the ones not in NBRL3D (yet) that bug me. Does anyone out there know how to go about this? Thanks in advance, Christoph -- Christoph Weber email: cweber@oci.unizh.ch OCI Uni Zurich phone: +41 1 257 4925 Winterthurerstr. 190 FAX: +41 1 361 9895 CH-8057 Zurich, Switzerland From owner-gcg@net.bio.net Thu Nov 03 22:00:00 1994 Newsgroups: bionet.software.gcg Path: biosci!agate!howland.reston.ans.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!rzusuntk.unizh.ch!birchaw From: birchaw@oci.unizh.ch (Birch Ashley) Subject: Q. ORFs on opposite strands Message-ID: <1994Nov4.150806.16559@rzu-news.unizh.ch> Sender: newsadm@rzu-news.unizh.ch (CNEWS ADMINISTRATION) Organization: University of Zurich, Switzerland X-Newsreader: TIN [version 1.2 PL2] Date: Fri, 4 Nov 1994 15:08:06 GMT Lines: 7 I have a problem with PUBLISH in version 7.3 Recently I wanted to use this program to generate a figure with a 5kb DNA sequence and several ORFs. The ORFs were non-overlapping but crucially were not all on the same strand i.e. I needed to get an aa sequence (ORF) under the sequence from say bp1500 to 3000 but also one travelling in the opposite direction from bp1200 to 400. There appears to be no facility to do this yet it must occur regularly. Am I doing something wrong or perhaps it can be done using ver sion 8.0. Anybody able to help me with this one? Much appreciated Ashley Birch E-Mail birchaw@oci.unizh.ch From owner-gcg@net.bio.net Thu Nov 03 22:00:00 1994 Path: biosci!rutgers!gatech!newsfeed.pitt.edu!dsinc!netnews.upenn.edu!cellbio05.med.upenn.edu!user From: user@a1.mscf.upenn.edu (User) Newsgroups: bionet.software.gcg,bionet.software.staden Subject: Digitizer input Date: Fri, 04 Nov 1994 14:58:56 -0500 Organization: Cell & Developmental Biology Lines: 21 Message-ID: NNTP-Posting-Host: cellbio05.med.upenn.edu Xref: biosci bionet.software.gcg:812 bionet.software.staden:24 Hi- We used a digitizer on a dedicated port to enter sequence directly in the GCG programs using seqed. My understanding is that gip in the staden package will do the same thing. This worked very well for us to enter DNA sequence data. My question now concerns mechanics of connections in a new environment. We don't have serial lines here at Penn (the whole campus is ethernet connected). We use powermacs and eXodus to connect to Sun computers which are running both GCG and the Staden programs. Does anyone know of a way to interface a sonic digitizer through our powermac over the network to these computers? This seems like the most straightforward solution to our sequence entry problem. A second possibility is to enter the data from digital images generated from either a scanner or phosphorimager. Does anyone know of software that might accomplish this? I am aware of HelisScan, DNA ProScan and the Bioimage software. Any others would be appreciated! Thanks! Brian Brunk U. Penn. School of Medicine Dept. of Cell and Devel. Biology 215-898-0243 brunkb@a1.mscf.upenn.edu From owner-gcg@net.bio.net Fri Nov 04 22:00:00 1994 Newsgroups: bionet.software.gcg Path: biosci!agate!spool.mu.edu!howland.reston.ans.net!pipex!sunic!ugle.unit.no!trane.uninett.no!eunet.no!nuug!EU.net!sun4nl!sci.kun.nl!caos.kun.nl!jackl From: jackl@caos.kun.nl (Jack Leunissen) Subject: Re: AA 3 letter to 1 letter code Message-ID: <1994Nov5.163544.27625@caos.kun.nl> Organization: CAOS/CAMM References: <1994Nov4.131358.11868@rzu-news.unizh.ch> Date: Sat, 5 Nov 1994 16:35:44 GMT Lines: 20 cweber@oci.unizh.ch (Christoph Weber) writes: >I have to pull out sequences from PDB files and get them into GCG format. I have program which reformats regular PDB-files into a NBRF formatted sequence database (i.e. in .seq, .ref, and -optionally- .ttl files). These can be used as a sequence database in GCG. Contact me if you want a copy... Regards, Jack -- +----------------------------------------------------------------+ Jack A.M. Leunissen, Ph.D. | CAOS/CAMM Center Email: jackl@caos.kun.nl | University of Nijmegen Tel. : +31 80 65 22 48 | Toernooiveld 1 Fax : +31 80 65 29 77 | 6525 ED Nijmegen, The Netherlands | URL=http://www.caos.kun.nl/ +-------- CAOS/CAMM is the Dutch National Node in EMBnet --------+ From owner-gcg@net.bio.net Sun Nov 06 22:00:00 1994 Path: biosci!agate!library.ucla.edu!europa.eng.gtefsd.com!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!sunsite.doc.ic.ac.uk!charlie.lif.icnet.uk!morpheus.lif.icnet.uk!user From: mike@bison.lif.icnet.uk (Mike Mitchell) Newsgroups: bionet.software.gcg Subject: SeqEd/PileUp problems with Telnet 2.5 Date: Mon, 07 Nov 1994 14:38:21 +0100 Organization: Imperial Cancer Research Fund Lines: 39 Message-ID: NNTP-Posting-Host: morpheus.lif.icnet.uk We are currently having a major problem with NCSA Telnet 2.5 (Mac) and the GCG sequence editors. Our system: Digital AXP OSF/1 GCG v8 Mac NCSA Telnet 2.5 When users try to use the arrow keys to move around a sequence capital letters are typed instead (D for <- etc..). If Telnet 2.6 or VersaTerm are used for the terminal emulation, this does not occur. Has any one found a solution to this, other than upgrading 600 Macs from 2.5 to 2.6? We have had a suggestion from GCG to set the terminal type within Telnet to vt200 or vt220. This stops the arrow keys from functioning at all! Thanx in advance for your help and time. -- * ***************************************************************** * *Michael Mitchell *"All I know about babies is that you * *User Support * are not supposed to put them into * *Molecular Biology Software * washing machines. Makes the colours * *Imperial Cancer Research Fund* run, presumably." * *+44 (0)71 269 3115 * Tom Holt - Here Comes The Sun - 1994* * ***************************************************************** * -- * ***************************************************************** * *Michael Mitchell *"All I know about babies is that you * *User Support * are not supposed to put them into * *Molecular Biology Software * washing machines. Makes the colours * *Imperial Cancer Research Fund* run, presumably." * *+44 (0)71 269 3115 * Tom Holt - Here Comes The Sun - 1994* * ***************************************************************** * From owner-gcg@net.bio.net Sun Nov 06 22:00:00 1994 Path: biosci!rutgers!gatech!europa.eng.gtefsd.com!news.umbc.edu!not-for-mail From: xlin@umbc.edu (Xiaoying Lin) Newsgroups: bionet.software.gcg Subject: Re: SeqEd/PileUp problems with Telnet 2.5 Date: 7 Nov 1994 14:45:36 -0500 Organization: University of Maryland, Baltimore County Lines: 51 Message-ID: <39m050$6ia@umbc7.umbc.edu> References: NNTP-Posting-Host: umbc7.umbc.edu I experinced similar problem with GCG v7 on iris. It was solved by adding the following command in my .gcgrc file. Do not know if it will work with v8. setenv TERM iris-ansi In article , Mike Mitchell wrote: >We are currently having a major problem with NCSA Telnet 2.5 (Mac) and >the GCG sequence editors. > >Our system: Digital AXP > OSF/1 > GCG v8 > Mac NCSA Telnet 2.5 > >When users try to use the arrow keys to move around a sequence capital >letters are typed instead (D for <- etc..). > >If Telnet 2.6 or VersaTerm are used for the terminal emulation, this does >not occur. > >Has any one found a solution to this, other than upgrading 600 Macs from >2.5 to 2.6? > >We have had a suggestion from GCG to set the terminal type within Telnet >to vt200 or vt220. This stops the arrow keys from functioning at all! > >Thanx in advance for your help and time. > >-- >* ***************************************************************** * >*Michael Mitchell *"All I know about babies is that you * >*User Support * are not supposed to put them into * >*Molecular Biology Software * washing machines. Makes the colours * >*Imperial Cancer Research Fund* run, presumably." * >*+44 (0)71 269 3115 * Tom Holt - Here Comes The Sun - 1994* >* ***************************************************************** * > >-- >* ***************************************************************** * >*Michael Mitchell *"All I know about babies is that you * >*User Support * are not supposed to put them into * >*Molecular Biology Software * washing machines. Makes the colours * >*Imperial Cancer Research Fund* run, presumably." * >*+44 (0)71 269 3115 * Tom Holt - Here Comes The Sun - 1994* >* ***************************************************************** * -- Xiaoying Xiaoying Lin Mail checked NIGHTly. From owner-gcg@net.bio.net Sun Nov 06 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!pipex!lyra.csx.cam.ac.uk!sunsite.doc.ic.ac.uk!charlie.lif.icnet.uk!news.lif.icnet.uk!alex From: alex@dapsun.lif.icnet.uk (Alex Whittaker) Newsgroups: bionet.software.gcg Subject: Seqed: Telnet 2.5 incompatibilities Date: 07 Nov 1994 14:50:57 GMT Organization: Imperial Cancer Research Fund Lines: 64 Distribution: world Message-ID: NNTP-Posting-Host: dapsun.lif.icnet.uk We are offering the GCG 8.0 release on our Digital AXP (Alpha) system running OSF/1 and are experiencing some difficulties with the Seqed/lineup software run over a Mac Telnet version 2.5 terminal. The problem is relates to the arrow keys which the mapping for which is changed from ^[[A ^[[B ^[[C and ^[[D to ^[OA ^[OB ^[OC and ^[OD. This is not interpreted correctly, and causes the editor to discard the escape O and print a capital A B C or D to the screen. As seqed is fairly essential to the running of a reasonable service, and most users connect through telnet 2.5 we are very concerned. I voiced these concerns to GCG and had the following response: > >We are familiar with this problem. The best way to solve it is to upgrade to >a >newer version of NCSA Telnet such as version 2.6. > >One thing that you can try is: > >Edit Config.tel (on the MAC) >termtype="vt200". > >Then log on to the unix system. For sun set term=vt200 for >irix set term=vt220. I'm not sure which to try on OSF. This does not work on >Ultrix, and since OSF is also from DEC it may not work their either. (but >you can take the sun terminfo entry for vt200 and compile it on the ultrix >machine and the arrow keys will work) > .. > >We never tracked down the exact source of the problem, and no longer have >version 2.5 for testing. > Although I appreciate that it is difficult to cater for differences in other peoples software, upgrading telnet accross arround 400 macs is not a short term solution. The alternative suggested modification to the config.tel file has the effect of turning off the arrow keys completely. Has anyone else been able to resolve this issue, could they share it with us. If not, can anyone suggest an alternative sequence editor in the public domain, compatible with our system. Regards, Alex Whittaker ______ \||/_ | | oo \ "All I know Biomedical Informatics Unit | | L_ is that I know Imperial Cancer Research Fund |______| \/ nothing" London ________ | [========] / alex@bison.lif.icnet.uk ---OOO- |ooooooo| -- Alex Whittaker ______ \||/_ | | oo \ "All I know Biomedical Informatics Unit | | L_ is that I know Imperial Cancer Research Fund |______| \/ nothing" London ________ | [========] / alex@bison.lif.icnet.uk ---OOO- |ooooooo| From owner-gcg@net.bio.net Mon Nov 07 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!EU.net!uknet!daresbury!not-for-mail From: mario garcia Newsgroups: bionet.software.gcg Subject: small molecule databases Date: 8 Nov 1994 12:51:43 -0000 Lines: 17 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <39ns8v$df6@mserv1.dl.ac.uk> Original-To: info-gcg@dl.ac.uk Hi everyone, Would anyone know if there is any free-access database holding structural information (i.e. 3-D coordinates or crystallographic data) about small organic molecules, such as penicillins and related molecules? Any kind of information regarding this subject will be nicely appreciated. Thanks for your help. --------------------------------------------------------------------------- Mario Garcia de Lacoba. Phone : +341 5611800 (ext.4334) Fax : +341 5627518 Centro de Investigaciones Biologicas E-mail : cibmg05@cc.csic.es C.S.I.C. C./ Velazquez, 144 28006-Madrid. SPAIN. --------------------------------------------------------------------------- From owner-gcg@net.bio.net Mon Nov 07 22:00:00 1994 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!yogi!doelz From: doelz@urz.unibas.ch (R.Doelz,Biocomputing Basel;+41 61 267 22 47) Newsgroups: bionet.software.gcg Subject: Re: Seqed: Telnet 2.5 incompatibilities Message-ID: <1994Nov8.200954.44151@yogi> Date: 8 Nov 94 20:09:54 MET References: Distribution: world Organization: University of Basel, Switzerland Lines: 58 In article , alex@dapsun.lif.icnet.uk (Alex Whittaker) writes: > We are offering the GCG 8.0 release on our Digital AXP (Alpha) system > running OSF/1 and are experiencing some difficulties with the Seqed/lineup > software run over a Mac Telnet version 2.5 terminal. The problem is > relates to the arrow keys which the mapping for which is changed from ^[[A > ^[[B ^[[C and ^[[D to ^[OA ^[OB ^[OC and ^[OD. This is not interpreted > correctly, and causes the editor to discard the escape O and print a > capital A B C or D to the screen. As seqed is fairly essential to the > running of a reasonable service, and most users connect through telnet 2.5 > we are very concerned. I voiced these concerns to GCG and had the > following response: >> >>One thing that you can try is: >> >>Edit Config.tel (on the MAC) >>termtype="vt200". ... >> >>Then log on to the unix system. For sun set term=vt200 for >>irix set term=vt220. I'm not sure which to try on OSF. This does not work on >>Ultrix, and since OSF is also from DEC it may not work their either. (but >>you can take the sun terminfo entry for vt200 and compile it on the ultrix >>machine and the arrow keys will work) >> > .. >> >>We never tracked down the exact source of the problem, and no longer have >>version 2.5 for testing. >> > > Although I appreciate that it is difficult to cater for differences in > other peoples software, upgrading telnet accross arround 400 macs is not a > short term solution. The alternative suggested modification to the > config.tel file has the effect of turning off the arrow keys completely. > > Has anyone else been able to resolve this issue, could they share it with > us. If not, can anyone suggest an alternative sequence editor in the > public domain, compatible with our system. > Macs at our site work happily with NCSA 2.5 and % setenv TERM ansi Reason being, that the 'termcap' entry on OSF/1 defines lots of padding and other things, e.g. a 5 milliseconds padding for relative cursor screen movement (cm=5\E[%i%d;%dH). The vt200 features are different and will kill the seqed program also. The 'ansi' definition does not have any of these features but is a 'ansi terminal with pessimistic assumptions' - however, I am not aware of possible ramifications of this setting. Maybe this helps Regards Reinhard Doelz EMBnet Switzerland From owner-gcg@net.bio.net Tue Nov 08 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!grapevine.lcs.mit.edu!uhog.mit.edu!europa.eng.gtefsd.com!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!msuinfo!harbinger.cc.monash.edu.au!bunyip.cc.uq.oz.au!munnari.oz.au!ariel.ucs.unimelb.EDU.AU!ucsvc.ucs.unimelb.edu.au!wehi.edu.au!wehi.edu.au!robert Newsgroups: bionet.software.gcg Subject: Profile - kinase.prf sequences? Message-ID: <1994Nov9.143225.1@wehi.edu.au> From: robert@wehi.edu.au (Robert Flegg) Date: 9 Nov 94 14:32:25 +1000 Organization: Database Consortium. ANSAF@WEHI/LICR/CSIRO/BRI NNTP-Posting-Host: wehit.wehi.edu.au Lines: 43 G'Day GCG provides a number of profiles for use with the PROFILESEARCH and PROFILESCAN programs. These profiles have been created by the PROFILEMAKE program, as reflected in the header of KINASE.PRF which is reproduced below. My question is - Does anybody know what are the sequences and database entry numbers of the seven sequences that have been used to construct this profile? > (Peptide) PROFILEMAKE v4.00 of: @kin.fil Length: 310 Sequences: 7 > MaxScore: 193.70 22-JUL-1988 15:49 > > Gap: 1.00 Len: 1.00 > GapRatio: 0.33 LenRatio: 0.10 > > okbog.frg From: 1 To: 310 Weight: 1.00 > okbo2c.frg From: 1 To: 310 Weight: 1.00 > kiboc.frg From: 1 To: 310 Weight: 1.00 > tvhuf6.frg From: 1 To: 310 Weight: 1.00 > tvhums.frg From: 1 To: 310 Weight: 1.00 > a24169.frg From: 1 To: 310 Weight: 1.00 > a24673.frg From: 1 To: 310 Weight: 1.00 > > Symbol comparison table: ProfilePep.cmp FileCheck: 975 I was unable to find any reference to the seven fragments, either online or in the GCG documentation. If it is there, and I missed it, then naturally I apologize - perhaps I should clean my glasses more often. Any help will be greatly appreciated. Regards Robert Flegg -- Robert Flegg |=| email: robert@wehi.edu.au Database Liaison Officer |=| flegg@ludwig.edu.au ANSAF @ WEHI/LICR/CSIRO/BRI |=| phone: (+61-3) 345-2618 From owner-gcg@net.bio.net Tue Nov 08 22:00:00 1994 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!nntp-serv.cam.ac.uk!pmr From: pmr@staffa.sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.gcg Subject: Re: Profile - kinase.prf sequences? Date: 09 Nov 1994 10:20:12 GMT Organization: University of Cambridge, England Lines: 52 Message-ID: References: <1994Nov9.143225.1@wehi.edu.au> NNTP-Posting-Host: staffa.sanger.ac.uk In-reply-to: robert@wehi.edu.au's message of 9 Nov 94 14:32:25 +1000 In article <1994Nov9.143225.1@wehi.edu.au> robert@wehi.edu.au (Robert Flegg) writes: > GCG provides a number of profiles for use with the PROFILESEARCH and > PROFILESCAN programs. These profiles have been created by the > PROFILEMAKE program, as reflected in the header of KINASE.PRF which > is reproduced below. > > My question is - Does anybody know what are the sequences and database > entry numbers of the seven sequences that have been > used to construct this profile? > > > (Peptide) PROFILEMAKE v4.00 of: @kin.fil Length: 310 Sequences: 7 > > MaxScore: 193.70 22-JUL-1988 15:49 > > > > Gap: 1.00 Len: 1.00 > > GapRatio: 0.33 LenRatio: 0.10 > > > > okbog.frg From: 1 To: 310 Weight: 1.00 > > okbo2c.frg From: 1 To: 310 Weight: 1.00 > > kiboc.frg From: 1 To: 310 Weight: 1.00 > > tvhuf6.frg From: 1 To: 310 Weight: 1.00 > > tvhums.frg From: 1 To: 310 Weight: 1.00 > > a24169.frg From: 1 To: 310 Weight: 1.00 > > a24673.frg From: 1 To: 310 Weight: 1.00 > > > > Symbol comparison table: ProfilePep.cmp FileCheck: 975 > > I was unable to find any reference to the seven fragments, either online or > in the GCG documentation. If it is there, and I missed it, then naturally > I apologize - perhaps I should clean my glasses more often. > > Any help will be greatly appreciated. The only folk who know the answer for sure are those who built the profile in 1988, "kin.fil" and the "*.frg" files are (were) on the system where the profile was made. The full sequences should be in PIR - the names look like PIR entry names and are indeed available in PIR (release 42). The last two are accession numbers from PIR. These now have entry names TVMSP1 and TVHUFF. You can find the subsequences with profilegap and then use PileUp to get at least close to the original alignments. -- ------------------------------------------------------------------------ Peter Rice | Informatics Division E-mail: pmr@sanger.ac.uk | The Sanger Centre Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, Fax: (44) 1223 494919 | Cambs, CB10 1RQ URL: http://www.sanger.ac.uk/~pmr | England From owner-gcg@net.bio.net Tue Nov 08 22:00:00 1994 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!usc!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!charlie.lif.icnet.uk!news.lif.icnet.uk!alex From: alex@darwin.lif.icnet.uk (Alex Whittaker - BIU) Newsgroups: bionet.software.gcg Subject: Re: Seqed: Telnet 2.5 incompatibilities Date: 09 Nov 1994 14:04:38 GMT Organization: Imperial Cancer Research Fund Lines: 32 Distribution: world Message-ID: NNTP-Posting-Host: darwin.lif.icnet.uk >Macs at our site work happily with NCSA 2.5 and >% setenv TERM ansi > >Reason being, that the 'termcap' entry on OSF/1 defines lots of >padding and other things, e.g. a 5 milliseconds padding for relative >cursor screen movement (cm=5\E[%i%d;%dH). The vt200 features are different >and will kill the seqed program also. The 'ansi' definition does not have >any of these features but is a 'ansi terminal with pessimistic assumptions' >- however, I am not aware of possible ramifications of this setting. Many thanks for that response, you were quite correct, and by modifying the seqed command to: OLDTERM=$TERM; TERM=ansi; seqed %1 %2 %3 %4 %5 %6 %7 %8 %9; TERM=$OLDTERM Other problems associated with loosing terminal type are also avoided. Regards, -- Alex Whittaker ______ \||/_ | | oo \ "All I know Biomedical Informatics Unit | | L_ is that I know Imperial Cancer Research Fund |______| \/ nothing" London ________ | [========] / alex@bison.lif.icnet.uk ---OOO- |ooooooo| From owner-gcg@net.bio.net Fri Nov 11 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!pipex!uunet!Germany.EU.net!news.dfn.de!rrz.uni-koeln.de!RRZ.Uni-Koeln.DE!a1624091 From: a1624091@athena.rrz.uni-koeln.de (Jan T. Kim) Newsgroups: bionet.software.gcg Subject: Questions: ASSEMBLE commandline and FINDPATTERNS Date: 12 Nov 1994 21:19:55 GMT Organization: Regional Computing Center, University of Cologne Lines: 48 Message-ID: <3a3bhrINN1id3@rs1.rrz.Uni-Koeln.DE> Reply-To: a1624091@athena.rrz.uni-koeln.de NNTP-Posting-Host: hpw1.rrz.uni-koeln.de X-Newsreader: Tin 1.1 PL5 Dear GCG gurus, I recently switched from using a VMS based GCG installation to using an OSF/1 based one. Under VMS, I used to create DCL command files that would call ASSEMBLE to retrieve pieces of sequences surrounding regions found by FINDPATTERNS. The DCL command sequences looked like: $ assemble myseq.Pep 62 171 no yes w myseq.mseq Now, under OSF/1, it is not possible pass image data to a program called from a shell script that easily (it is probably feasible to have the script create a file with the image data and redirect ASSEMBLE's stdin to that file, but that seems messy to me). I tried to specify all parameters in the command line: assemble -begin=62 -end=171 -outfile=myseq.mseq myseq.pep However, ASSEMBLE still asks for the beginning of the segment interactively. What is wrong? I'd like to make two remarks: (1) While messing around with ASSEMBLE, I found that it is possible to specify any nonsense option witout eliciting any warning or complaint. Is this normal? (2) My entire problem would disappear if there was a method to tell FINDPATTERNS to retrieve sequence segments beginning at some offset from the first matching symbol and extending for some arbitrary length for each match found. My current method to achieve this is a program I wrote which scans a *.find file created by FINDPATTERNS and produces a DCL command procedure as described above. I ran into the problem while adapting this hack of mine to generate a shell script in place of the DCL procedure. Greetinx & many thanx in advance, Jan -- +- Jan Kim -- X.400: S=kim;OU=vax;O=mpiz-koeln;P=mpg;A=d400;C=de -+ | Internet: kim@vax.mpiz-koeln.mpg.d400.de | | | *-----=< hierarchical systems are for files, not for humans >=-----* From owner-gcg@net.bio.net Sun Nov 13 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!lyra.csx.cam.ac.uk!nntp-serv.cam.ac.uk!pmr From: pmr@staffa.sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.gcg Subject: Re: Questions: ASSEMBLE commandline and FINDPATTERNS Date: 14 Nov 1994 10:16:50 GMT Organization: University of Cambridge, England Lines: 60 Message-ID: References: <3a3bhrINN1id3@rs1.rrz.Uni-Koeln.DE> NNTP-Posting-Host: staffa.sanger.ac.uk In-reply-to: a1624091@athena.rrz.uni-koeln.de's message of 12 Nov 1994 21:19:55 GMT a1624091@athena.rrz.uni-koeln.de (Jan T. Kim) writes: > > assemble -begin=62 -end=171 -outfile=myseq.mseq myseq.pep > >However, ASSEMBLE still asks for the beginning of the segment >interactively. What is wrong? The program continues to prompt for a second segment. If you put -default on the command line the program will stop after the first segment. >I'd like to make two remarks: > >(1) While messing around with ASSEMBLE, I found that it is possible >to specify any nonsense option witout eliciting any warning or >complaint. Is this normal? This is normal, and was even the case under VMS because GCG does not use the standard DCL command line parsing. Of course once you put -default on the command line the program asks no questions and you always have to check the output carefully to be sure the command line was correct. >(2) My entire problem would disappear if there was a method to tell >FINDPATTERNS to retrieve sequence segments beginning at some offset >from the first matching symbol and extending for some arbitrary >length for each match found. My current method to achieve this is >a program I wrote which scans a *.find file created by FINDPATTERNS >and produces a DCL command procedure as described above. I ran >into the problem while adapting this hack of mine to generate a >shell script in place of the DCL procedure. Not to sure what you want here, but perhaps the problem is that FINDPATTERNS always writes 5 residues before and after the hit. This, for some reason, is hardcoded into GenApplib:showhits.f You could work around this by extending the pattern with the required number of X positions. These will match anything, and will be reported as part of the hit. One problem with this approach is that you will miss any hits that do not have enough flanking residues, but you can catch those by running without the Xs. Perhaps a future version will let you specify the extra 5 residues before and after the hits on the command line - quite easily done by a change to the showhits function. ------------------------------------------------------------------------ Peter Rice | Informatics Division E-mail: pmr@sanger.ac.uk | The Sanger Centre Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, Fax: (44) 1223 494919 | Cambs, CB10 1RQ URL: http://www.sanger.ac.uk/~pmr | England -- ------------------------------------------------------------------------ Peter Rice | Informatics Division E-mail: pmr@sanger.ac.uk | The Sanger Centre Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, Fax: (44) 1223 494919 | Cambs, CB10 1RQ URL: http://www.sanger.ac.uk/~pmr | England From owner-gcg@net.bio.net Wed Nov 16 22:00:00 1994 Path: biosci!MOLBIO.CBS.UMN.EDU!jknott From: jknott@MOLBIO.CBS.UMN.EDU (Julie Knott) Newsgroups: bionet.software.gcg Subject: Re: Pileup problem with long sequences Date: 16 Nov 1994 17:32:39 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 25 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <1994Nov16.180235.1@crcvms.unl.edu> NNTP-Posting-Host: net.bio.net Jay, PileUp's maximum sequence length is 5kb. I don't know if it can be changed. It's a lousy parameter, as I have 10-20kb I'd like to see too. Please let me know if you find a better way. I'll be watching the net -- does anyone know a better way? Julie jknott@molbio.cbs.umn.edu On 16 Nov 1994 jcalvert@crcvms.unl.edu wrote: > What's the most likely cause of the "alignment may not > be optimal" message during a pileup alignment of several > long sequences? The resulting output is clearly not the > best alignment. Is this a memory problem? What parameter > needs to be increased? > > Thanks in advance for helpful suggestions from anyone. > > Jay Calvert jcalvert@crcvms.unl.edu > > > From owner-gcg@net.bio.net Wed Nov 16 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!pipex!uunet!ulowell!aspen.uml.edu!bradleys From: bradleys@aspen.uml.edu Newsgroups: bionet.software.gcg Subject: Acquisition? Date: 17 Nov 94 13:14:54 -0500 Organization: University of Massachusetts Lowell Lines: 3 Message-ID: <1994Nov17.131454.1@aspen.uml.edu> NNTP-Posting-Host: aspen.uml.edu Can someone send me info. for acquiring GCG? Thanx Sean From owner-gcg@net.bio.net Wed Nov 16 22:00:00 1994 Path: biosci!ugene1.abbott.com!bollingt From: bollingt@ugene1.abbott.com (Tim Bolling) Newsgroups: bionet.software.gcg Subject: Re: pileup Date: 16 Nov 1994 17:47:43 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: <9411170146.AA18882@ugene1.abbott.com> NNTP-Posting-Host: net.bio.net You have to change the configuration that is included in the pileupconstants.inc file and then rebuild the pileup application. We use the follow values around here... Integer MAXSTRBUFF Parameter ( MAXSTRBUFF = 8 000 000) Integer MAXSURFACE Parameter ( MAXSURFACE = 16 000 000) Integer SEGDEF Parameter ( SEGDEF = 10000 ) Integer PADDINGDEF Parameter ( PADDINGDEF = 10000 ) The above is for Unix GCG-version8.0. From owner-gcg@net.bio.net Wed Nov 16 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!vixen.cso.uiuc.edu!newsfeed.ksu.ksu.edu!moe.ksu.ksu.edu!crcnis1.unl.edu!crcvms.unl.edu!jcalvert From: jcalvert@crcvms.unl.edu Newsgroups: bionet.software.gcg Subject: Pileup problem with long sequences Date: 16 Nov 94 18:02:35 CST Organization: University of Nebraska--Lincoln Lines: 10 Message-ID: <1994Nov16.180235.1@crcvms.unl.edu> NNTP-Posting-Host: crcvms.unl.edu What's the most likely cause of the "alignment may not be optimal" message during a pileup alignment of several long sequences? The resulting output is clearly not the best alignment. Is this a memory problem? What parameter needs to be increased? Thanks in advance for helpful suggestions from anyone. Jay Calvert jcalvert@crcvms.unl.edu From owner-gcg@net.bio.net Thu Nov 17 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!news.sprintlink.net!tracker.ramp.com!dial-in-4-ts0.amug.org!user From: dvweiss@amug.org (Dennis V. Weiss, M.D.) Newsgroups: bionet.software.gcg Subject: Plate tectonics software Date: Thu, 17 Nov 1994 18:05:06 -0700 Organization: OnRamp Incorporated. Lines: 19 Message-ID: NNTP-Posting-Host: dial-in-4-ts0.amug.org > I need some help from the Internet surfers out there. My business partner > is helping the Science Museum with a project related to Plate Tectonics. > He is looking for software which is able to track/display the movement of > plates since this is going to be an interactive display. His preference > is for Mac software, but anything PC-based will do. > > The only one he's heard about is something that a company called Terra > Mobiles had about 4-6 years ago. Could you pass this request on to any of > the Geology/Geography/etc. groups that you know of. Replies can be sent > directly back to me, if you prefer at jklorman@fc.mcnet.com. > > Thanx, JK -- Dennis V. Weiss, M.D. dvweiss@amug.org Compu$erve 72774,2347 From owner-gcg@net.bio.net Fri Nov 18 22:00:00 1994 Path: biosci!agate!library.ucla.edu!ucsbuxb.ucsb.edu!mcl!uramzzzz From: uramzzzz@mcl.ucsb.edu (Ramzi Azzam) Newsgroups: bionet.software.gcg Subject: Questions about fasta searches? Date: 19 Nov 1994 00:33:06 GMT Organization: University of California, Santa Barbara Lines: 9 Message-ID: <3ajh42$iua@ucsbuxb.ucsb.edu> NNTP-Posting-Host: mcl.mcl.ucsb.edu Summary: I would like to know if there is a wa Keywords: fasta search parameters restrictions I would like to know if there is a way to restrict the search when using fasta. my problem is that I want to search using a 26bp segment of DNA that contains a central CG bp. I want each sequence selected by fasta to contain this CG and to penalize any sequence not containing the CG such that it does not appear in the best score list. If any one has any ideas on how to do this, it will be greatly appreciated and thanks in advance. my e-mail address is uramzzzz@mcl.mcl.ucsb.edu From owner-gcg@net.bio.net Fri Nov 18 22:00:00 1994 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.gcg Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 19 Nov 1994 02:00:12 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 322 Sender: daemon@net.bio.net Distribution: world Message-ID: <199411191000.CAA17154@net.bio.net> NNTP-Posting-Host: net.bio.net Four important items follow: How to cancel e-mail subscriptions to BIOSCI newsgroups, BIOSCI archive searching, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our BIOSCI user directory, please take a few minutes to complete and return the form below. If your personal information has changed since you listed yourself, please send us a complete new updated form. We can not make manual revisions to existing entries. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net **** How to cancel a BIOSCI e-mail subscription **** If you want to cancel your e-mail subscription to this group, PLEASE DO NOT POST YOUR UNSUBSCRIBE REQUEST TO THE NEWSGROUP ADDRESS (NOR REPLY TO A MESSAGE POSTED TO THE NEWSGROUP)!!! This would send your request to all of the readers of the newsgroup, but it might still not be seen by the BIOSCI staff - thus you would annoy many people and possibly not accomplish your goal anyway. 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Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: From owner-gcg@net.bio.net Mon Nov 21 22:00:00 1994 Path: biosci!uoguelph.ca!shzhang From: shzhang@uoguelph.ca (Shula Zhang) Newsgroups: bionet.software.gcg Subject: (none) Date: 22 Nov 1994 13:46:08 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hi, netters Could anyone tell me how and where I can get a free GCG or PCG or any other DNA/protein analysis software? Thank you. From owner-gcg@net.bio.net Mon Nov 21 22:00:00 1994 Path: biosci!MBIMAIL.UMD.EDU!belas From: belas@MBIMAIL.UMD.EDU ("Bob Belas") Newsgroups: bionet.software.gcg Subject: signoff Date: 22 Nov 1994 09:11:48 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: world Message-ID: <9410227855.AA785535049@mbimail.umd.edu> NNTP-Posting-Host: net.bio.net signoff info-gcg From owner-gcg@net.bio.net Mon Nov 21 22:00:00 1994 Path: biosci!agate!howland.reston.ans.net!swrinde!pipex!lyra.csx.cam.ac.uk!nntp-serv.cam.ac.uk!pmr From: pmr@staffa.sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.gcg,bionet.software.staden Subject: Re: Mapping motifs on one DNA strand only Followup-To: bionet.software.gcg,bionet.software.staden Date: 22 Nov 1994 15:51:54 GMT Organization: University of Cambridge, England Lines: 32 Message-ID: References: NNTP-Posting-Host: staffa.sanger.ac.uk In-reply-to: es@trefle.isv.cnrs-gif.fr's message of Tue, 22 Nov 1994 13:59:03 +0000 Xref: biosci bionet.software.gcg:831 bionet.software.staden:29 In article es@trefle.isv.cnrs-gif.fr (Eric Schoonejans) writes: > I have been using mapplot (from gcg) to locate and visualise small motifs > in DNA sequences. The way i did it was to create a .dat file of patterns > like > > motifA 1 ATCG 0 ! > motifB 1 ACGT 0 ! > > etc..., which can be read by the program and it will then display a nice > plot of the occurences of the motifs. > > My problem and hence my question is that it will search both strands for > each motif, like it would do for restriction enzymes sites. When the motif > is self complementary, like ACGT, no problem, but when it is not, it will > actually map the motif plus all occurences of its complementary motif like > ATCG _and_ CGAT. > So, is there a way to manipulate the file of motifs or the program to avoid > this or is there any alternative to display occurences of motifs on a DNA > sequence? > (Mac, VMS, Unix or PC; GCG or freeware only). You can use the same pattern file with findpatterns which has a command line option -onestrand Not graphical, but you get the positions. -- ------------------------------------------------------------------------ Peter Rice | Informatics Division E-mail: pmr@sanger.ac.uk | The Sanger Centre Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, Fax: (44) 1223 494919 | Cambs, CB10 1RQ URL: http://www.sanger.ac.uk/~pmr | England From owner-gcg@net.bio.net Mon Nov 21 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!citi2.fr!jussieu.fr!univ-lille1.fr!zaphod.crihan.fr!u-psud.fr!mac301.isv.cnrs-gif.fr!user From: es@trefle.isv.cnrs-gif.fr (Eric Schoonejans) Newsgroups: bionet.software.gcg,bionet.software.staden Subject: Re: Mapping motifs on one DNA strand only Followup-To: bionet.software,bionet.software.gcg,bionet.software.staden Date: Tue, 22 Nov 1994 19:50:24 +0000 Organization: ISV CNRS Lines: 37 Message-ID: References: NNTP-Posting-Host: mac301.isv.cnrs-gif.fr Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Xref: biosci bionet.software.gcg:833 bionet.software.staden:31 In article , pmr@staffa.sanger.ac.uk (Peter Rice) wrote: > In article es@trefle.isv.cnrs-gif.fr (Eric Schoonejans) writes: > > I have been using mapplot (from gcg) to locate and visualise small motifs > > in DNA sequences. some deleted > > My problem and hence my question is that it will search both strands for > > each motif, like it would do for restriction enzymes sites. When the motif > > is self complementary, like ACGT, no problem, but when it is not, it will > > actually map the motif plus all occurences of its complementary motif like > > ATCG _and_ CGAT. > > So, is there a way to manipulate the file of motifs or the program to avoid > > this or is there any alternative to display occurences of motifs on a DNA ^ graphically > > sequence? > > (Mac, VMS, Unix or PC; GCG or freeware only). (Or Staden package, by the way) > > You can use the same pattern file with findpatterns which has a command line > option -onestrand > > Not graphical, but you get the positions. > -- I forgot to mention that I _need_ a graphical display (to eye detect and visualize non random distribution of the motifs along the sequence). Thanks again Eric Schoonejans Institut des Sciences Vegetales CNRS - Gif sur Yvette - France From owner-gcg@net.bio.net Thu Nov 24 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!daresbury!not-for-mail From: mario garcia Newsgroups: bionet.software.gcg Subject: searching databases Date: 25 Nov 1994 11:04:58 -0000 Lines: 19 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3b4gcq$14t@mserv1.dl.ac.uk> Original-To: info-gcg@dl.ac.uk Hi everybody, I have two different questions: 1.- Does anyone know if there is any way to search a protein sequences database (e.g. Swissprot) using as query term the aminoacidic composition? 2.- Is there any computer program allowing to compare (graphically or not) two distinct RNA secondary structures? Any kind of information regarding some of the above questions will be gratefully appreciate. Thanks in advance. --------------------------------------------------------------------------- Mario Garcia de Lacoba. Phone : +341 5611800 (ext.4334) Fax : +341 5627518 Centro de Investigaciones Biologicas E-mail : cibmg05@cc.csic.es C.S.I.C. C./ Velazquez, 144 28006-Madrid. SPAIN. --------------------------------------------------------------------------- From owner-gcg@net.bio.net Thu Nov 24 22:00:00 1994 Path: biosci!MBIMAIL.UMD.EDU!belas From: belas@MBIMAIL.UMD.EDU ("Bob Belas") Newsgroups: bionet.software.gcg Subject: Re: searching databases Date: 25 Nov 1994 06:02:13 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: <9410257857.AA785782915@mbimail.umd.edu> NNTP-Posting-Host: net.bio.net I'd like to remove my name from the list. How is that done? Bob From owner-gcg@net.bio.net Fri Nov 25 22:00:00 1994 Path: biosci!MBIMAIL.UMD.EDU!belas From: belas@MBIMAIL.UMD.EDU ("Bob Belas") Newsgroups: bionet.software.gcg Subject: (none) Date: 26 Nov 1994 06:32:00 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: <9410267858.AA785871109@mbimail.umd.edu> NNTP-Posting-Host: net.bio.net signoff info-gcg unsubscribe info-gcg From owner-gcg@net.bio.net Fri Nov 25 22:00:00 1994 Newsgroups: bionet.software.gcg Path: biosci!agate!sunsite.doc.ic.ac.uk!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!rzusuntk.unizh.ch!rmf From: rmf@ikc.unizh.ch (Roman Fried) Subject: pileup with coding sequence Message-ID: <1994Nov26.101756.11503@rzu-news.unizh.ch> Sender: newsadm@rzu-news.unizh.ch (CNEWS ADMINISTRATION) Organization: University of Zurich, Switzerland X-Newsreader: TIN [version 1.2 PL2] Date: Sat, 26 Nov 1994 10:17:56 GMT Lines: 23 Hi Everybody I have some sequences containing introns. Now i would like to cut out the non-coding sequences and run pileup with the resulting sequences. Could someone mail me the easiest way how to do this? Many thanks in advance Regards Roman Roman Fried Institut fuer Klinische Chemie Universitaetsspital Zuerich 8091 Zuerich Tel 01/255 31 60 Fax 01/255 45 90 Net rmf@ikc.unizh.ch From owner-gcg@net.bio.net Sat Nov 26 22:00:00 1994 Path: biosci!MCRCR6.MED.NYU.EDU!HILLJ01 From: HILLJ01@MCRCR6.MED.NYU.EDU (John Edward Hill) Newsgroups: bionet.software.gcg Subject: Re: MSF as input to plotsimilarity Date: 27 Nov 1994 15:10:55 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 41 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <1994Nov27.211822.11466@emba.uvm.edu> NNTP-Posting-Host: net.bio.net For GCG8 (and GCG7, as I remember), you can use a msf file from PILEUP, but you have to use the GCG syntax for indicating which sequences from the msf file you want. For example, if you want all the sequences you would say: $ plotsimilarity pileup.msf{*} It's a great way to scan for regions of similarity vs. differences across the multiple alignment as a whole. Good luck! John ___________________________________________________________________________ John Edward Hill, Ph.D. | Department of Cell Biology Internet: hillj01@mcrcr.med.nyu.edu | New York University Medical Center EARN/Bitnet: HILL@NYUMED.BITNET | 550 First Avenue 212-263-7135 FAX: 212-263-8139 | New York, New York 10016 ___________________________________________________________________________ On Sun, 27 Nov 1994, Brian Foley wrote: > The documentation says that the output created by PILEUP > (the pileup.msf file) can be used as input to PLOTSIMILARITY. > > However, this is not working for me. PLOTSIM says it cannot > read pileup.msf. The documantation also says that all the sequences > have to be the same length, and my PILEUP was of sequences of > various lengths, gaps were introduced. Could this be the problem? > If so, how does one plot the similarity of proteins that have > udergone deletions/insertions during evolution? > > > -- > ******************************************************************** > * Brian Foley * If we knew what we were doing * > * Molecular Genetics Dept. * it wouldn't be called research * > * University of Vermont * * > ******************************************************************** > > From owner-gcg@net.bio.net Sat Nov 26 22:00:00 1994 Newsgroups: bionet.software.gcg Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!pipex!uunet!emba-news.uvm.edu!brianf From: brianf@med.uvm.edu (Brian Foley) Subject: MSF as input to plotsimilarity Message-ID: <1994Nov27.211822.11466@emba.uvm.edu> Sender: news@emba.uvm.edu Organization: EMBA Computer Facility, University of Vermont X-Newsreader: TIN [version 1.2 PL1] Date: Sun, 27 Nov 1994 21:18:22 GMT Lines: 17 The documentation says that the output created by PILEUP (the pileup.msf file) can be used as input to PLOTSIMILARITY. However, this is not working for me. PLOTSIM says it cannot read pileup.msf. The documantation also says that all the sequences have to be the same length, and my PILEUP was of sequences of various lengths, gaps were introduced. Could this be the problem? If so, how does one plot the similarity of proteins that have udergone deletions/insertions during evolution? -- ******************************************************************** * Brian Foley * If we knew what we were doing * * Molecular Genetics Dept. * it wouldn't be called research * * University of Vermont * * ******************************************************************** From owner-gcg@net.bio.net Sun Nov 27 22:00:00 1994 Newsgroups: bionet.software.gcg Path: biosci!agate!dog.ee.lbl.gov!news.cs.utah.edu!emba-news.uvm.edu!brianf From: brianf@med.uvm.edu (Brian Foley) Subject: Re: MSF as input to plotsimilarity Message-ID: <1994Nov28.005604.18959@emba.uvm.edu> Sender: news@emba.uvm.edu Organization: EMBA Computer Facility, University of Vermont X-Newsreader: TIN [version 1.2 PL1] References: <1994Nov27.211822.11466@emba.uvm.edu> Date: Mon, 28 Nov 1994 00:56:04 GMT Lines: 19 John Edward Hill (HILLJ01@MCRCR6.MED.NYU.EDU) wrote: : For GCG8 (and GCG7, as I remember), you can use a msf file from PILEUP, : but you have to use the GCG syntax for indicating which sequences from the : msf file you want. For example, if you want all the sequences you would : say: : $ plotsimilarity pileup.msf{*} Yes. This does work fine. I learn something new every day, but rarely from reading the UWGCG documentation. I'm sure the above info is in there somewhere (under "file syntax" perhaps?) but it was not to be found under the documentation on plotsimilarity. Perhaps it could be added to the EXAMPLE of PLOTSIMILARITY, those examples are usually the fastest way to figure out how to use a particular module. Thanks, John Hill, for the speedy reply! From owner-gcg@net.bio.net Sun Nov 27 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!wupost!waikato!comp.vuw.ac.nz!canterbury.ac.nz!chmeds.ac.nz!gordon From: gordon@chmeds.ac.nz Newsgroups: bionet.software.gcg Subject: VMS or Unix version? Message-ID: <1994Nov28.161608.723@chmeds.ac.nz> Date: 28 Nov 94 16:16:08 +1200 Lines: 20 A mixed group of scientists here has proposed purchasing GCG, running on an Alpha workstation of some description. My question is which operating system: OSF/1 (Unix by any other name would smell as sweet) or OpenVMS? We are probably more familiar with VMS; arguements are advanced that most of the tools for molecular biology are being developed in a Unix environment. Against this, I've ported several to VMS with minimal trouble. I'm interested in your opinions and prejudices on this issue. Slainte Gordon -- Gordon Findlay, Computer Scientist, Christchurch School of Medicine Nuclear-free New Zealand !SYSTEM-F-TOOMANFING Email: Gordon@CHMEDS.AC.NZ !Error: too many Paper: PO Box 4345, Christchurch, NEW ZEALAND !fingers on keyboard Voice: +64-3-364 0540 ! From owner-gcg@net.bio.net Sun Nov 27 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!pipex!uunet!psinntp!barilvm!vms.huji.ac.il!agri.huji.ac.il!dvorah Newsgroups: bionet.software.gcg Subject: Xterminal emulator for gcg 8 Message-ID: <28NOV199409481306@agri.huji.ac.il> From: dvorah@agri.huji.ac.il (DVORAH ART) Date: 28 Nov 1994 09:48 GMT Distribution: world Organization: The Hebrew University of Jerusalem Nntp-Posting-Host: agri.huji.ac.il News-Software: VAX/VMS VNEWS 1.41 Lines: 15 What X terminal program for Mac (MacX, eXodus, any others) have people had success using with gcg 8? For that matter, under Microsoft Windows running on winsock? The only winsock x-terminal we're aware of is PCXware. Are there otheres? What are their pros and cons? Please send replies directly to me, the news server sometimes looses items. Thanks Deborah Weisman dvorah@agri.huji.ac.il From owner-gcg@net.bio.net Mon Nov 28 22:00:00 1994 Path: biosci!agate!overload.lbl.gov!dog.ee.lbl.gov!news.cs.utah.edu!news.cc.utah.edu!ls-28.biology.utah.edu!user From: kofoid@biology.utah.edu (Eric Kofoid) Newsgroups: bionet.software.gcg Subject: Re: Xterminal emulator for gcg 8 Date: Tue, 29 Nov 1994 10:10:18 -0700 Organization: Dept. Biology, University of Utah Lines: 23 Distribution: world Message-ID: References: <28NOV199409481306@agri.huji.ac.il> NNTP-Posting-Host: ls-28.biology.utah.edu In article <28NOV199409481306@agri.huji.ac.il>, dvorah@agri.huji.ac.il (DVORAH ART) wrote: -What X terminal program for Mac (MacX, eXodus, any others) -have people had success using with gcg 8? -For that matter, under Microsoft Windows running on winsock? -The only winsock x-terminal we're aware of is PCXware. Are there -otheres? What are their pros and cons? - - -Please send replies directly to me, the news server sometimes looses -items. - -Thanks - -Deborah Weisman -dvorah@agri.huji.ac.il MacX works just fine. We've run v.8.0 under it for several months now. Cheers, Eric. From owner-gcg@net.bio.net Mon Nov 28 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!uhog.mit.edu!europa.eng.gtefsd.com!howland.reston.ans.net!pipex!sunic!trane.uninett.no!eunet.no!nuug!dkuug!dkuug!dkbbbs!lars.thomsen From: lars.thomsen@dkb.dk (LARS THOMSEN) Newsgroups: bionet.software.gcg Subject: Data aquisition Message-ID: <89EA0BE.0E5F000045.uuout@dkb.dk> Date: Tue, 29 Nov 94 03:10:00 +0100 Distribution: world Organization: Danish Key Board BBS - Copenhagen Denmark - +45 3325 5600 Reply-To: lars.thomsen@dkb.dk (LARS THOMSEN) X-Newsreader: PCBoard Version 15.2 X-Mailer: PCBoard/UUOUT Version 1.0 Lines: 35 To : All I am using a data-acquisition system from Cambridge Electronic Design, to record from my current-clamp setup. The interface is a separate 20 MHz computer with some sort of parallel port to my PC. The interface has 32 A/D ports, 4 D/A, and 16 TTL. And a lot of external clocks, and event triggers that I never use. The program to control the interface is called Spike2 (capture module), and it has "pulse program" consisting of 256 programming lines to control the TTL's and the D/A ports. The data acquisition is working almost perfect, but I am having problems with the "pulse program". What I want to do is to control my electrophysiological setup totally from the PC's keyboard. The pulseprogram has no variables, which means that if I want to make to inject 0.5 nA into my neurone, then I need to write 0.5 nA, and if I want 0.6 nA then this is another line. That means that I have run out of lines. What I want is a variable for e.g. injecting current and the ability to increase and decrease this variable by pressing e.g. the arrowkeys at the keyboard. I am in fact controlling my setup with this "pulse program", but I would like to be able to make some fine tuning. Anyone who knows a system that is perfect for this task ? I would be very happy if you wrote some details ! Best Regards MSc Lars Thomsen Royal Veterinary & Agricultural University Copenhagen, Denmark --- þ CMPQwk #1.4þ UNREGISTERED EVALUATION COPY From owner-gcg@net.bio.net Mon Nov 28 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!msuinfo!netnews.upenn.edu!hmivax!bailey From: bailey@genetics.upenn.edu (Charles Bailey) Newsgroups: bionet.software.gcg Subject: Re: VMS or Unix version? Date: 28 Nov 94 21:03:33 EST Organization: HHMI/Human Genetics, Univ of Pa. Lines: 48 Message-ID: <1994Nov28.210333@hmivax> References: <1994Nov28.161608.723@chmeds.ac.nz> NNTP-Posting-Host: hmivax.humgen.upenn.edu In article <1994Nov28.161608.723@chmeds.ac.nz>, gordon@chmeds.ac.nz writes: > A mixed group of scientists here has proposed purchasing GCG, running on > an Alpha workstation of some description. > > My question is which operating system: OSF/1 (Unix by any other name would > smell as sweet) or OpenVMS? > > We are probably more familiar with VMS; arguements are advanced that most of > the tools for molecular biology are being developed in a Unix environment. > Against this, I've ported several to VMS with minimal trouble. > > I'm interested in your opinions and prejudices on this issue. I'm not sure there's a general answer to this question. You'll need to make the decision based on the particular needs of your site, comfort of users, etc. You've said that your users are more familiar with VMS, and implied that the major use for the system would be GCG, which is perfectly comfortable under VMS. (Some would say it is more comfortable under VMS than Unix.) This would appear to make VMS the right choice for you. While I agree that a lot of the biological software out there is being developed on Unix systems, much of it does port to VMS without major headaches (and, for the most part, fie on the authors of that which doesn't, but that's another thread . . .). There are a few trouble spots - Unix-specific system calls, required toolkits (e.g. what's up with Tcl/Tk in the VMS world?), but I don't think the possibility that porting some future application to VMS would be difficult is enough reason to avoid an OS which will make most of your users happier. Finally, if you've settled on an AXP, the decision isn't as binding as it might otherwise be - if you decide to changes OSs in the future, just install the new software. If your university participates in DEC's educational licensing programs, the cost of the changeover will probably be small. Finally, the disclaimer - while I'm speaking only for myself, and have no connection to DEC, I'm an unabashed fan of the AXP and VMS. If only DEC could get out from under terminally shortsighted planning and marketing . . . Caveat lector. Regards, Charles Bailey !------------------------------------------------------------------------------- ! Computational Biology and Informatics Laboratory ! Dept. of Genetics, Univ. of Pennsylvania School of Medicine ! Philadelphia, PA USA 19104 Tel. (215) 573-3112 ! Internet: bailey@genetics.upenn.edu (IN 128.91.200.37) !------------------------------------------------------------------------------- From owner-gcg@net.bio.net Mon Nov 28 22:00:00 1994 Path: biosci!AC.DAL.CA!HCHENG From: HCHENG@AC.DAL.CA Newsgroups: bionet.software.gcg Subject: sign on Date: 29 Nov 1994 01:56:11 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HK0TO7000I017CQ1@AC.DAL.CA> NNTP-Posting-Host: net.bio.net subscribe info-gcg Hong Cheng From owner-gcg@net.bio.net Mon Nov 28 22:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!news.doit.wisc.edu!news From: dalehn@facstaff.wisc.edu (Donald A. Lehn, Ph.D.) Newsgroups: bionet.software.gcg Subject: Re: VMS or Unix version? Date: Tue, 29 Nov 94 13:23:41 EST Organization: University of Wisconsin Medical School Lines: 30 Message-ID: <3bfvfa$gr@news.doit.wisc.edu> References: <1994Nov28.161608.723@chmeds.ac.nz> <1994Nov28.210333@hmivax> NNTP-Posting-Host: islet.medsch.wisc.edu Mime-Version: 1.0 X-Newsreader: WinVN 0.93.6 In article <1994Nov28.210333@hmivax>, bailey@genetics.upenn.edu says... > >In article <1994Nov28.161608.723@chmeds.ac.nz>, gordon@chmeds.ac.nz writes: >> A mixed group of scientists here has proposed purchasing GCG, running on >> an Alpha workstation of some description. >> > >Finally, if you've settled on an AXP, the decision isn't as binding as it might >otherwise be - if you decide to changes OSs in the future, just install the >new software. If your university participates in DEC's educational licensing >programs, the cost of the changeover will probably be small. > Just a general question about the Unix version of GCG. Is it posix (sp?) compliant and will it run under Windows NT on the Alpha workstation? It seems to me that this would be a great system since the computer could be put to use as a "general" Windows computer when it is not being used to run the GCG package (something thats not easy with VMS). -- Donald A. Lehn, Ph.D. Phone: (608) 263-7668 Medical Sciences Center / 3415 Fax: (608) 262-9300 University of Wisconsin Medical School Email: dalehn@facstaff.wisc.edu 1300 University Avenue Home: (608) 277-1025 Madison, WI 53706-1532 <<<<<<< No, I'm not a real doctor -- I just teach 'em! >>>>>>> From owner-gcg@net.bio.net Tue Nov 29 22:00:00 1994 Newsgroups: bionet.software.gcg Path: biosci!rutgers!gatech!howland.reston.ans.net!news.moneng.mei.com!uwm.edu!lll-winken.llnl.gov!overload.lbl.gov!dog.ee.lbl.gov!news.cs.utah.edu!emba-news.uvm.edu!sadye!aquilla From: aquilla@salus.med.uvm.edu (Tracy Aquilla) Subject: Re: : SKILL CONTEST - WIN $750,000 CONDO! Message-ID: Sender: news@emba.uvm.edu Organization: EMBA Computer Facility, University of Vermont X-Newsreader: VersaTerm Link v1.1 References: <25.25.2387@datanet.com> Date: Tue, 29 Nov 1994 21:46:54 GMT Lines: 28 In Article <25.25.2387@datanet.com>, contest@datanet.com (Contest) wrote: > > ******** WIN ********* > LUXURY 4BR PENTHOUSE > MARINA DEL REY, CA. USA > VALUED AT $725,000 > > Steps to beach-near LAX Located within exclusive Los Angeles, CA. > Marina Peninsula. area Home to movie, TV, and sports celebrities. > 3350 sq. ft. + 1200' private sun deck, 3 fireplaces, > 4 and 1/2 baths library/den, bar and game room. > Winner is determined by simple contest of skill. > Limited to 4000 entries. $250 entrance fee. > > For application & details send Internet EMail to CONTEST@DATANET.COM > > > DNIS - Palm Springs, California * Via Modem Call: (619) 864-1468 > A Winner Of The 1993 John C. Dvorak Telecommunications Award!! > How many Usenet groups have you posted this message to? Please stop sending us this garbage! It is a waste of bandwidth, and I find it annoying. Tracy Aquilla, Ph.D. Molecular Physiology and Biophysics University of Vermont aquilla@salus.med.uvm.edu From owner-gcg@net.bio.net Wed Nov 30 22:00:00 1994 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!pipex!uknet!comlab.ox.ac.uk!oxuniv!jrees From: jrees@vax.oxford.ac.uk (Jasper Rees - Oxford University) Newsgroups: bionet.software.gcg Subject: Re: VMS or Unix version? Message-ID: <1994Nov30.232829.27843@oxvaxd> Date: 30 Nov 94 23:28:29 GMT References: <1994Nov28.161608.723@chmeds.ac.nz> <1994Nov28.210333@hmivax> <3bfvfa$gr@news.doit.wisc.edu> Organization: Oxford University VAX 6620 Lines: 40 In article <3bfvfa$gr@news.doit.wisc.edu>, dalehn@facstaff.wisc.edu (Donald A. Lehn, Ph.D.) writes: > > Just a general question about the Unix version of GCG. Is it posix (sp?) > compliant Doubt it. Did you ever see any real software that was? :)) Put another way, GCG does not use posix to get VMS/unix compatibility. > and will it run under Windows NT on the Alpha workstation? No. Not yet. No doubt at some time in the future. Probably when there is a perceived marketplace for it. > It seems to me that this would be a great system since the computer > could be put to use as a "general" Windows computer when it is not > being used to run the GCG package (something thats not easy with VMS). Depends what you use your computers for I guess, here we use ours for 600+ users for GCG and other assorted molbiol stuff and have one facility for the whole campus, and that keeps them fully utilised for most of the time. We find Macs and PC's do the "general" stuff on the desktop quite nicely thank you, (read we do not run wordperfect on our molbiol system :)) while your average desktop machine is ill suited to running hundreds of hours of phylogenetic calculations, which are a major feature of the system utilisation here. > Donald A. Lehn, Ph.D. Phone: (608) 263-7668 jasper D Jasper G Rees MA DPhil You are in a twisty little maze of Wellcome Senior Research Fellow cDNA clones, all different. The Sir William Dunn School of Pathology You are characterising the ones Oxford University most like talin..... South Parks Road Oxford, OX1 3RE, United Kingdom Tel: +44 1865 275567 FAX: +44 1865 275501 Email: Jasper.Rees@Pathology.Oxford.Ac.UK From owner-gcg@net.bio.net Wed Nov 30 22:00:00 1994 Path: biosci!uoguelph.ca!shzhang From: shzhang@uoguelph.ca (Shula Zhang) Newsgroups: bionet.software.gcg Subject: (none) Date: 30 Nov 1994 17:32:12 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hi, netters Could you tell me from where I can get e-mail service for GCG analyses. Thank you.