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Re: [Gusdev-gusdev] Similarity table changes
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From: Jonathan S. <js...@pc...> - 2004-07-19 15:50:10
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Sucheta: That info is in the NA (or AA) Sequence table. Remember that the query and subject sequences can be in different external_database_releases so that info must be on the individual sequences, not the similarity. Jonathan On Jul 19, 2004, at 11:26 AM, Sucheta Tripathy wrote: > Hi Jonathan, > > Our databases are not really having any sequence overlap. So as you > suggested the external_database_release_id should be fine. But when I > look into the Dots.similarity and the dots.similarityspan I don't see > anything pointing to externaldatabase/externaldatabaserelease. I was > wondering if I missed out something or there is a linker. > > Thanks > > Sucheta > > At 10:00 AM 7/19/2004 -0400, Jonathan Schug wrote: >> Sucheta, and All: >> >> If the blast libraries do not overlap, i.e., contain different sets of >> sequences, then there is probably no problem. You can simply >> distinguish the Similarity rows by the target sequence's >> external_database_release_id. >> >> If the libraries overlap, then the issue is more difficult. We don't >> have the notion of a library in this sense, and of course the library >> size affects the p-values for matches. There is a DoTS::Library table >> that holds clone information that could be hacked to provide what you >> want, but I do *not* recommend it as a long term solution. You could >> also use the DoTS::DbRefNaSequence or DoTS::AASequenceDbRef as >> appropriate to link to a DoTS::DbRef which links to an >> ExternalDatabase. These tables could easily be used to gather >> sequences into multiple BLAST database files. >> >> The best solution is probably to create new tables. >> >> I propose, then the following changes to the Similarity table and the >> addition of new table to track search libraries: >> >> DoTS::Similarity >> - add search_algorithm_invocation_id link to stably point to >> parameter values for the search. >> >> SRes::SearchLibrary >> - contains a description of the search library including entry count >> etc. >> >> SRes::SearchLibraryMember >> - uses a soft link, i.e., table_id, row_id to indicate membership. >> - link is soft so that SearchLibrary can also be used for motifs, >> etc. that may not be in sequence table. >> - SearchLibrary might contain a table_id to record what kind of >> entries are in the library. >> >> Thoughts? >> >> Jonathan >> >> On Jul 19, 2004, at 9:31 AM, Sucheta Tripathy wrote: >> >>> Hi Jonathan, >>> >>> Thanks for your reply. I also have a similar concern which I posted >>> sometimes back. My concern is to do with multiple databases rather >>> than the parameters for blast search. Currently we want to store >>> blast >>> results against 23 different databases. Any suggestions which table >>> may be suitable? >>> >>> Thanks >>> >>> Sucheta >>> >>> At 12:18 AM 7/19/2004 -0400, Jonathan Schug wrote: >>>> Josef: >>>> >>>> The two columns in DoTS::Similarity that might be useful are >>>> algorithm >>>> and row_alg_invocation_id. Algorithm is not recommended; it is >>>> meant >>>> to be used to distinguish, say, BLAST hits from FASTA hits. >>>> Row_alg_invocation_id is better and will work. You can use the >>>> AlgoithmInvocation parameters. However, this will not work if the >>>> rows >>>> are modified in some way later one. Later updates will change the >>>> row_alg_invocation_id ruining this scheme. You could also consider >>>> linking Similarity rows to the invocation via an Evidence row. This >>>> is >>>> more stable. >>>> >>>> PlasmoDB faced this when tuning BLAST parameters to avoid the >>>> problems >>>> with the high AT content of the Pf genome. They may have tuned the >>>> parameters outside of the DB. >>>> >>>> You might also consider running the BLAST searches with the most >>>> lenient parameters, then recreating the more stringent searches with >>>> query parameters if this is possible >>>> >>>> Jonathan >>>> >>>> >>>> -------------------------------------------------------------------- >>>> -- -- --- >>>> Jonathan Schug Center for Bioinformatics >>>> js...@pc... Computational Biology and Informatics Lab >>>> (215) 573-3113 voice University of Pennsylvania, >>>> (215) 573-3111 fax 1413 Blockley Hall, Philadelphia, PA >>>> 19014-6021 >>>> >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------- >>>> This SF.Net email is sponsored by BEA Weblogic Workshop >>>> FREE Java Enterprise J2EE developer tools! >>>> Get your free copy of BEA WebLogic Workshop 8.1 today. >>>> http://ads.osdn.com/?ad_id=4721&alloc_id=10040&op=click >>>> _______________________________________________ >>>> Gusdev-gusdev mailing list >>>> Gus...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> >> >> ------------------------------------------------------- >> This SF.Net email is sponsored by BEA Weblogic Workshop >> FREE Java Enterprise J2EE developer tools! >> Get your free copy of BEA WebLogic Workshop 8.1 today. >> http://ads.osdn.com/?ad_id=4721&alloc_id=10040&op=click >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
