Re: [Gusdev-gusdev] Similarity table changes

[Sucheta T. <su...@vb...>]

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
>>>
>>>
>>>
>>>
>>>
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