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

Joe Landman bioclusters@bioinformatics.org
Fri, 10 Sep 2004 09:37:48 -0400

Kevin Karplus wrote:

>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).

Hi Kevin:

  That was a little tongue-in-cheek on my part.  I should have used an 
emoticon.  :(  My point was simply that if the data he needed was there, 
probably he could avoid worrying about the rest, as long as the 
information he was getting out was accurate relative to his calculation. 


Joseph Landman, Ph.D
Scalable Informatics LLC,
email: landman@scalableinformatics.com
web  : http://www.scalableinformatics.com
phone: +1 734 612 4615