[ssml] Re: [Bioclusters] mpiBLAST and NCBI Blast? BioseqFindFunc: couldn't uncache

[Kevin Karplus]

Joseph Landman wrote
> Hmm.  Does it impact the output data you need (actual alignment 
> information), or are you after parameters and computational "side 
> effects" (bit scores, E-values,...)

Careful of your assumptions here!  For many of us the E-values and IDs
arethe only useful data out of BLAST, with the alignments being so
poor as to be discarded.  This is a common enough usage of blast that
there is even an output format for it (-m 9 is the format I use).

------------------------------------------------------------
Kevin Karplus 	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
Senior member, IEEE	Board of Directors, ISCB (starting Jan 2005)
Professor of Biomolecular Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
Affiliations for identification only.