Hello, Dennis.
The calculation you should be using is referenced in
http://genome.ucsc.edu/FAQ/FAQblat.html#blat4. The relevant portion of the script is:
my $pslScore = $sizeMul * ($matches + ( $repMatches >> 1) ) - $sizeMul * $misMatches - $qNumInsert - $tNumInsert;
The value of sizeMul is either 3 or 1 depending on whether or not your query is a protein sequence or not. Since we're not dealing with a protein sequence, the value of sizeMul is 1, so the formula is essentially:
pslScore = #matches - #misMatches - #qInserts - #tInserts
Based on what you described, it sounds like the score is roughly what it should be.
If there is still confusion, could you let us know whether you're using gfServer with hgBlat, standalone blat or something else? Also, please provide your query sequence and the name of the assembly you're querying so we can attempt to replicate your query.
Please contact us again at
gen...@soe.ucsc.edu if you have any further questions. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to
genom...@soe.ucsc.edu.
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Steve Heitner
UCSC Genome Bioinformatics Group
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