From owner-embldatabank@net.bio.net Thu Jul 04 23:00:00 1996 Path: biosci!biosci!not-for-mail From: DSF <76042.532@CompuServe.COM> Newsgroups: bionet.genome.chromosomes,bionet.molbio.embldatabank,bionet.molbio.genbank,bionet.molbio.methds-reagnts Subject: QIAGEN MINIPREP ROBOT Date: 4 Jul 1996 23:40:21 -0700 Organization: Cadus Lines: 4 Sender: biohelp@net.bio.net Distribution: world Message-ID: <4qu5he$c0k$1@mhafc.production.compuserve.com> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.genome.chromosomes:1251 bionet.molbio.embldatabank:656 bionet.molbio.genbank:2320 bionet.molbio.methds-reagnts:46536 Has anyone had any experience with the qiagen miniprep robots especially with regards to sequencing on the abi sequencers (373 and 377) please reply by e-mail. thank you From owner-embldatabank@net.bio.net Thu Jul 04 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!news-res.gsl.net!news.gsl.net!hunter.premier.net!newsfeed.internetmci.com!swrinde!tank.news.pipex.net!pipex!oleane!in2p3.fr!swidir.switch.ch!scsing.switch.ch!news.belwue.de!fu-berlin.de!cs.tu-berlin.de!uni-erlangen.de!lrz-muenchen.de!ipp-garching.mpg.de!wanze!souza From: souza@wanze (Augustine Souza) Newsgroups: bionet.genome.chromosomes,bionet.molbio.embldatabank,bionet.molbio.genbank,bionet.molbio.methds-reagnts Subject: Re: QIAGEN MINIPREP ROBOT Followup-To: bionet.genome.chromosomes,bionet.molbio.embldatabank,bionet.molbio.genbank,bionet.molbio.methds-reagnts Date: 5 Jul 1996 14:22:32 GMT Organization: Rechenzentrum der Max-Planck-Gesellschaft in Garching Lines: 9 Distribution: world Message-ID: <4rj8f8$6eoe@sat.ipp-garching.mpg.de> References: <4qu5he$c0k$1@mhafc.production.compuserve.com> NNTP-Posting-Host: wanze.biochem.mpg.de X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.genome.chromosomes:1252 bionet.molbio.embldatabank:657 bionet.molbio.genbank:2321 bionet.molbio.methds-reagnts:46552 DSF (76042.532@CompuServe.COM) wrote: : Has anyone had any experience with the qiagen miniprep robots : especially with regards to sequencing on the abi sequencers (373 : and 377) please reply by e-mail. : thank you Why don't you get a postdoc? Gus From owner-embldatabank@net.bio.net Mon Jul 08 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!nntp.coast.net!news00.sunet.se!sunic!news99.sunet.se!columba.udac.uu.se!evolution!thomas From: Thomas Sicheritz Newsgroups: bionet.molbio.embldatabank,bionet.software Subject: Script for extracting genes ? Date: Tue, 9 Jul 1996 13:49:38 +0200 Organization: Uppsala University Lines: 33 Message-ID: NNTP-Posting-Host: evolution.bmc.uu.se Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: thomas@evolution Xref: biosci bionet.molbio.embldatabank:658 bionet.software:16041 Hej, I need a script/program which can scan an EMBL or Genbank file and extract all gene names with start-stop, length, type, direction ... (maybe exon information too) the output should be something like that: rice chloroplast: name type dir start stop length rps16:x2:2 CDS R 4487 4635 148 rps16:x1:2 CDS R 5514 5553 39 trnQ tRNA R 6615 6687 72 psbK CDS F 7033 7218 185 psbI CDS F 7608 7718 110 trnS tRNA R 7829 7916 87 ORF100 CDS F 8349 8651 302 has anybody seen or written such a script/program (in perl,tcl,C,C++) ? thx -thomas Sicheritz Ponten Thomas E. UPPSALA UNIVERSITY Vangsbyvaegen 128 S-740 20 Vaenge Biomedical Center Home: +46 18 364358 Department of Molecular Biology BMC: +46 18 174379 BOX 590 S-751 24 UPPSALA Sweden Fax +46 18 557723 http://skydancer.bmc.uu.se/~thomas Chaos always defeats order, because it is better organized. (Terry Pratchett) From owner-embldatabank@net.bio.net Sun Jul 21 23:00:00 1996 Newsgroups: bionet.molbio.embldatabank,bionet.software Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!sgigate.sgi.com!nntp.coast.net!news-res.gsl.net!news.gsl.net!hunter.premier.net!news.cais.net!nntp.primenet.com!uunet!inXS.uu.net!comp.vuw.ac.nz!HERMES!TP.grace.cri.nz!cookj From: cookj@landcare.cri.nz (Jeremy Cook) Subject: Re: Script for extracting genes ? Message-ID: Date: Mon, 22 Jul 1996 15:51:10 References: Organization: Landcare Research X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Lines: 33 Xref: biosci bionet.molbio.embldatabank:662 bionet.software:16147 In article Thomas Sicheritz writes: >From: Thomas Sicheritz >Subject: Script for extracting genes ? >Date: Tue, 9 Jul 1996 13:49:38 +0200 >Hej, >I need a script/program which can scan an EMBL or Genbank file and >extract all gene names with start-stop, length, type, direction ... >(maybe exon information too) >the output should be something like that: >rice chloroplast: >name type dir start stop length >rps16:x2:2 CDS R 4487 4635 148 >rps16:x1:2 CDS R 5514 5553 39 >trnQ tRNA R 6615 6687 72 >psbK CDS F 7033 7218 185 >psbI CDS F 7608 7718 110 >trnS tRNA R 7829 7916 87 >ORF100 CDS F 8349 8651 302 >has anybody seen or written such a script/program (in perl,tcl,C,C++) ? >thx >-thomas Are all this required data held in these EMBL or Genbank files, and are these two source formats text? Jeremy From owner-embldatabank@net.bio.net Sun Jul 21 23:00:00 1996 Path: biosci!agate!news.ucdavis.edu!info.ucla.edu!newshub.sdsu.edu!newsfeeder.sdsu.edu!sgigate.sgi.com!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!panix!news.columbia.edu!news From: rf Newsgroups: bionet.molbio.embldatabank Subject: Re: Script for extracting genes ? Date: Mon, 22 Jul 1996 12:35:34 +0100 Organization: Columbia University Lines: 14 Message-ID: <31F36786.475B@you.too> NNTP-Posting-Host: ghostwriter.ccc.columbia.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Macintosh; I; PPC) Dear Thomas, There is a number of gene identification programs available in the "Grail" series. Try writing grailmai@mars.epm.ornl.gov with your question. The programs require fasta input so that you'll have to translate your file. I believe there are programs in GCG that does this. -Rich Richard A. Friedman Senior User Services Consultant Columbia Presbyterian Cancer Center From owner-embldatabank@net.bio.net Sun Jul 21 23:00:00 1996 Path: biosci!agate!news.ucdavis.edu!info.ucla.edu!newshub.sdsu.edu!newsfeeder.sdsu.edu!sgigate.sgi.com!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!panix!news.columbia.edu!news From: rf Newsgroups: bionet.molbio.embldatabank,bionet.software Subject: Re: Script for extracting genes ? Date: Mon, 22 Jul 1996 12:41:03 +0100 Organization: Columbia University Lines: 12 Message-ID: <31F368CF.164F@you.too> References: NNTP-Posting-Host: ghostwriter.ccc.columbia.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Macintosh; I; PPC) Xref: biosci bionet.molbio.embldatabank:664 bionet.software:16150 Dear Thomas, Write grailmai@mars.epm.ornl.gov with your questions and they will tell you about programs. You will probably have to translate from Genbank to fasta format. I believe that there are programs in GCG that can do that. Best Wishes Rich Richard A. Friedman Senior User Services Consultant Columbia Unioversit Cancer Center Computer Facility