[Bioclusters] sensitivity & blast

Pamela Culpepper pculpep at hotmail.com
Wed Apr 6 16:39:12 EDT 2005

Lik Mui,

More testing reveals that the -Y option works as follows.
In the absense of -Y, the "effective search space" is the product of the 
query sequence length
and the total database length.  It affects the calculation of the expection 
value but not the score.
It will thus vary with the query sequence length.
Using "-Y 12345" sets the above "effective search space" to 12345, constant 
for each query
sequence.   To make the expectation roughly reflect match length, one could 
use a -Y value
that is the product of  the database size and the longest query sequence 

Pam and Bill

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