[Genome] BLAT program

Jittima Piriyapongsa gtg894p at mail.gatech.edu
Wed Apr 4 14:14:35 PDT 2007


Hi,

I have a question regarding BLAT search 
(http://genome.ucsc.edu/cgi-bin/hgBlat?command=start). What is the 
default cut-off value for the program?  I saw in the details on the 
same page mentioned that BLAT quickly find sequences of 95% and 
greater similarity of length 40 bases or more. The results I got 
sometimes have hits with lower identity (i.e, 80% identity) or with 
short span length (i.e. ~20). Is it possible to know what is the 
exact cut-off values you used?

Thank you very much.
Jittima 



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