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Re: [GUSDEV] RE: Gusdev-gusdev digest, Vol 1 #637 - 1 msg
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From: Chris S. <sto...@pc...> - 2005-08-04 18:56:39
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Hi Sanjeev, I guess the first thing to decide is if this entry represents a sequence, a feature, or an annotation. Do you (or anyone else) have strong opinions on this? Can you send an example entry? Thanks, Chris On Aug 4, 2005, at 12:35 PM, Kumar, Sanjeev (Contr) wrote: > Hi, > Now let us figure out which GUS table to used to store PrositeDB > master data. > Can any one help me in that please? > Following type of information it contains: > ID Identification (Begins each entry; 1 per entry) > AC Accession number (1 per entry) > DT Date (1 per entry) > DE Short description (1 per entry) > PA Pattern (>1 per entry) > MA Matrix/profile (>1 per entry) > RU Rule (>1 per entry) > NR Numerical results (>1 per entry) > CC Comments (>=1 per entry) > DR Cross-references to Swiss-Prot (>1 per entry) > 3D Cross-references to PDB (>1 per entry) > DO Pointer to the documentation file (1 per entry) > > Any help on this will be appreciated. > > > Thanks > Sanjeev > > -----Original Message----- > From: gus...@li... > [mailto:gus...@li...]On Behalf Of > gus...@li... > Sent: Tuesday, August 02, 2005 11:09 PM > To: gus...@li... > Subject: Gusdev-gusdev digest, Vol 1 #637 - 1 msg > > > Send Gusdev-gusdev mailing list submissions to > gus...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > or, via email, send a message with subject or body 'help' to > gus...@li... > > You can reach the person managing the list at > gus...@li... > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Gusdev-gusdev digest..." > > > Today's Topics: > > 1. RE: Loading Prosite DB (Kumar, Sanjeev (Contr)) > > --__--__-- > > Message: 1 > Subject: RE: [GUSDEV] Loading Prosite DB > Date: Tue, 2 Aug 2005 17:04:05 -0400 > From: "Kumar, Sanjeev \(Contr\)" <San...@ng...> > To: "Aaron J. Mackey" <am...@pc...> > Cc: "Jian Lu" <jl...@vb...>, > <gus...@li...> > > So, The PlugIn which you are writing will not be taking care detail = > Prosite data, right? > If yes then I will write a separate plugin to load detail Prosite > master = > data. > > Thanks > Sanjeev > > -----Original Message----- > From: Aaron J. Mackey [mailto:am...@pc...] > Sent: Tuesday, August 02, 2005 5:01 PM > To: Kumar, Sanjeev (Contr) > Cc: Jian Lu; gus...@li... > Subject: Re: [GUSDEV] Loading Prosite DB > > > Yes, InterProScan only provides domain analysis results, not the =20 > actual domain/pattern/motif databases themselves. > > -Aaron > > On Aug 2, 2005, at 4:54 PM, Kumar, Sanjeev (Contr) wrote: > > >> Hi Aaron/Jian, >> The Interproscan data has only PrositeID and description in it. >> =20 >> But to load other information for a prosite ID, we need to load >> the =20 >> Prosite data which comes in different format than Interpro. >> That is what I found, Do you copy? >> >> Thanks >> Sanjeev >> >> -----Original Message----- >> From: Aaron J. Mackey [mailto:am...@pc...] >> Sent: Tuesday, August 02, 2005 4:43 PM >> To: Jian Lu >> Cc: Kumar, Sanjeev (Contr) >> Subject: Re: [GUSDEV] Loading Prosite DB >> >> >> >> From http://www.ebi.ac.uk/interpro/README1.html >> >> PROSITE patterns. >> >> Some biologically significant amino acid patterns can be summarised >> in the form of regular expressions. >> >> ScanRegExp (by Wol...@eb...), Ppsearch (Fuchs, R. >> 1994) . >> >> PROSITE profile. >> >> There are a number of protein families as well as functional or >> structural domains that cannot be detected using patterns due to >> their extreme sequence divergence; the use of techniques based on >> weight matrices (also known as profiles) allows the detection of such >> domains. >> >> pfscan from thePftools package (by Phi...@is...). >> >> PRINTS. >> The PRINTS database houses a collection of protein family >> fingerprints. These are groups of motifs that together are >> diagnostically more potent than single motifs by making use of the >> biological context inherent in a multiple-motif method. >> >> FingerPRINTScan (Scordis, P. et al. 1999) . >> >> PFAM. >> Pfam is a database of protein domain families. Pfam contains curated >> multiple sequence alignments for each family and corresponding >> profile hidden Markov models (HMMs). >> >> hmmpfam from theHMMER2.1 package (by Sean Eddy, >> ed...@ge..., http://hmmer.wustl.edu), >> DeCypher=99 (TimeLogic) implementation of HMM search. >> >> PRODOM. >> ProDom families are built by an automated process based on a >> recursive use ofPSI-BLAST homology searches. >> >> BlastProDom.pl (by Florence Servant, fse...@to...) >> =96 a filter on top of theBlast package (Altschul, S. F. et al. >> 1997) = >> > . > >> >> SMART. >> SMART domains are extensively annotated with respect to phyletic >> distributions, functional class, tertiary structures and functionally >> important residues. SMART alignments are optimised manually and >> following construction of corresponding hidden Markov models (HMMs). >> >> hmmpfam from theHMMER2.1 package. >> >> TIGRFAMs. >> TIGRFAMs are a collection of protein families featuring curated >> multiple sequence alignments, Hidden Markov Models (HMMs) and >> associated information designed to support the automated functional >> identification of proteins by sequence homology. Classification by >> equivalog family (see below), where achievable, complements >> classification by orthologs, superfamily, domain or motif. It >> provides the information best suited for automatic assignment of >> specific functions to proteins from large scale genome sequencing >> projects >> >> =D8 hmmpfam from theHMMER2.1 package. >> >> Optionally, predictions for coiled-coil, signal peptide cleavage >> sites (SignalP v2) and TM helices (TMHMM v2) are supported. >> >> >> >> On Aug 2, 2005, at 4:32 PM, Jian Lu wrote: >> >> >> >>> I don't think so. Here is the data sheet from InterProScan. >>> >>> Kumar, Sanjeev (Contr) wrote: >>> >>> >>> >>> >>>> Hi Aaron/Jian, >>>> What all types of data we are talking in IterProScan plugin? >>>> Does it include Prosite data. >>>> Thanks >>>> Sanjeev >>>> >>>> -----Original Message----- >>>> From: Jian Lu [mailto:jl...@vb...] >>>> Sent: Tuesday, August 02, 2005 2:02 PM >>>> To: Aaron J. Mackey >>>> Cc: Kumar, Sanjeev (Contr); gus...@li... >>>> Subject: Re: [GUSDEV] Loading Prosite DB >>>> >>>> >>>> Aaron, >>>> >>>> We are also working on InterProScan and other analysis tools. But >>>> we haven't got a plugin yet. If your plugin is ready, I would like >>>> to play it. Here is the view that we created for InterProScan. >>>> Please comment it. Thanks. >>>> >>>> -- >>>> -- VIEW DOTS.INTERPROSCAN >>>> -- used to store outputs from InterProScan >>>> -- June 29, 2005 >>>> >>>> >>>> >>>> >>> >>> >>> <InterProScan_OUTPUT.pdf> >>> >>> >>> >> >> -- >> Aaron J. Mackey, Ph.D. >> Project Manager, ApiDB Bioinformatics Resource Center >> Penn Genomics Institute, University of Pennsylvania >> email: am...@pc... >> office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI) >> fax: 215-746-6697 >> postal: Penn Genomics Institute >> Goddard Labs 212 >> 415 S. University Avenue >> Philadelphia, PA 19104-6017 >> >> >> >> >> ------------------------------------------------------- >> SF.Net email is sponsored by: Discover Easy Linux Migration >> Strategies >> from IBM. Find simple to follow Roadmaps, straightforward articles, >> informative Webcasts and more! Get everything you need to get up to >> speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=CCk >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> > > -- > Aaron J. Mackey, Ph.D. > Project Manager, ApiDB Bioinformatics Resource Center > Penn Genomics Institute, University of Pennsylvania > email: am...@pc... > office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI) > fax: 215-746-6697 > postal: Penn Genomics Institute > Goddard Labs 212 > 415 S. University Avenue > Philadelphia, PA 19104-6017 > > > > > > --__--__-- > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > End of Gusdev-gusdev Digest > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle > Practices > Agile & Plan-Driven Development * Managing Projects & Teams * > Testing & QA > Security * Process Improvement & Measurement * http://www.sqe.com/ > bsce5sf > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
