Re: [Gusdev-gusdev] Multiple blast analyses - few options

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

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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