[Genome] Question regarding parsing BLAT search result

[Yavatkar, Amarendra (NIH/NINDS) [C]]

Hello,

 

I have a question regarding computing score value using psl out put.  I
am using gfClient locally and generating .psl, .pslx, and pslpretty
files.  I would really if you could guide me computing scores based on
matches.  I am looking at getting an output similar to webBlat with top
three scores, start, and end values and the sequence output with the
matchning results for top three scores.

 

Thanks,

 

Amar

 

Amarendra S. Yavatkar 
Bioinformatics Project Lead (Contractor) 
SRA International Inc. 
NIH/ NINDS/ DIR/ ITP 
Building 10, Room 4N256 
10 Center Drive MSC 1392 
Bethesda, MD 20892-1392 
Phone: 301-402-1790 
e-mail: yavatka at ninds.nih.gov