[Gusdev-gusdev] Multiple blast analyses - few options

[Jonathan S. <js...@pc...>]

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


------------------------------------------------------------------------ 
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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