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Article #436Re: GCG non-support
From: Peter Rice
Date: Fri, 03 Aug 2007 21:55
Date: Fri, 03 Aug 2007 21:55
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3483 bytes
Steve Thompson wrote: >> Can you make a quick list of the additional functionality you would >> like to see [in GDE]? I seem to recall "rich sequence format" was one >> of GCG's major extensions. > > Yes, some have already been mentioned in this thread; I think these two > are the most important: > > 1) The ability to directly load sequence data from output sequence lists > from other programs such as BLAST, FastA, and a reference searching > program (in GCG that is the SRS derivative LookUp) with the option of > trimming that data to the length id'ed by a similarity search. As Nick > mentioned this ability to handle "ad-hoc" databases can be very powerful. That input should be simple (something like EMBL:X13776) and the code is relatively easy to do > 2) The ability to display FEATURE information from database entries in > colored and graphical representations. This is especially helpful for > homology inference of active sites and secondary structure. That was the part that used "rich sequence format" to store rearranged features and markup. I expect it can be reproduced using GFF as the feature standard (EMBOSS uses GFF internally, it is a good fit with even the EMBL/Genbank/DDBJ feature table and extendable for colouring etc - Artemis does something similar) > Too bad, but I'm glad there are alternatives. Perhaps some variation of > NCBI's stand alone Entrez, but it is designed for ASN.1 data . . . . . Or MRS from CMBI in Nijmegen. Or something using web services. There are many possibilities. Peter
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X-Google-Thread: 10a7a9,a153fb95848c03ee X-Google-Attributes: gid10a7a9,public,usenet X-Google-Language: ENGLISH,ASCII-7-bit Path: arc1-ca.pugleaf.net!g2news2.google.com!news2.google.com!newsfeed.stanford.edu!elk.ncren.net!news.purdue.edu!not-for-mail From: Peter Rice <pmr@ebi.ac.uk> Newsgroups: bionet.molbio.evolution Subject: Re: GCG non-support Date: Fri, 03 Aug 2007 22:55:10 +0100 Organization: European Bioinformatics institute Lines: 37 Approved: BIOSCI Approval Key <biosci-approval-key@net.bio.net> Message-ID: <mailman.519.1186178412.11350.mol-evol@net.bio.net> References: <C2D6445A.54FA%staffa@niehs.nih.gov> <mailman.471.1186000851.11350.bio-soft@net.bio.net> <46B1AEA8.2040308@ebi.ac.uk> <20070802081845.D3246@epsilon.bio.fsu.edu> <46B2F2E3.4020305@ebi.ac.uk> <20070803131050.H7747@epsilon.bio.fsu.edu> NNTP-Posting-Host: kalo.bio.indiana.edu Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Trace: mailhub227.itcs.purdue.edu 1186178441 14730 129.79.224.26 (3 Aug 2007 22:00:41 GMT) X-Complaints-To: news@purdue.edu NNTP-Posting-Date: Fri, 3 Aug 2007 22:00:41 +0000 (UTC) Cc: mol-evol@magpie.bio.indiana.edu, bio-soft@magpie.bio.indiana.edu, info-gcg@magpie.bio.indiana.edu, comp-bio@magpie.bio.indiana.edu To: Steve Thompson <stevet@bio.fsu.edu> X-Envelope-From: pmr@ebi.ac.uk User-Agent: Thunderbird 2.0.0.5 (X11/20070719) In-Reply-To: <20070803131050.H7747@epsilon.bio.fsu.edu> X-Mailman-Approved-At: Fri, 03 Aug 2007 17:00:10 -0500 X-BeenThere: mol-evol@net.bio.net X-Mailman-Version: 2.1.4 Precedence: list X-Auth: PGPMoose V1.1 PGP bionet.molbio.evolution iQCVAwUBRrOlbKCIqsWvyF5FAQE/GQQAv+3W1cBgWUH/Sod5xpMNc8L7Jh/Ycf8t WJ8qS+xBT7YRMesQq9PgNT8tfCrJHTu0AAZ3zGzE64UnW09LGKQyOQOywWNrc8n9 Jd8B2adswXDbhVFPWoewQq4YcjwLMVVe0ptGYWasaLMtv3uAhP84Xrzy+y9RaIMq x3Ogm+dQK5Q= =Ft0M