[Genome] parameters for Blat

[Brooke Rhead]

Hello Mi-Kyung,

Thank you for the compliments on BLAT.

Please see the BLAT specifications located here:

http://genome.ucsc.edu/goldenPath/help/blatSpec.html

as well as our BLAT FAQ section:

http://genome.ucsc.edu/FAQ/FAQblat

I also asked one of our developers for some usage examples for minScore, 
minIdentity and minAli.  Here is his response:

=====
-minAli is a parameter to pslReps.

In pslReps, it's used as follows:

int milliMin = 1000*minAli;
if (calcMilliScore(psl) >= milliMin

int calcMilliScore(struct psl *psl)
/* Figure out percentage score. */
{
return 1000-pslCalcMilliBad(psl, TRUE);
}

pslCalcMilliBad() is in the blat faq.
===
(which you can see in the second link I gave above)

===
So the minAli takes into account overall coverage
and acts like a score.  For mRNA against genome,
it is roughly like
  keep if
    (1 - ((mismatches+#qgaps)/matches))) > minAli

-minIdentity is sometimes not much use alone in
filtering because identity is often very high
and many alignments have high identity ON
the parts that DO align.  Parts that don't
align are not even considered by minIdentity.
So minIdentity has little effect on the overall
completeness of coverage.
=====

I hope this information is helpful.  Please feel free to write back to 
this list if we can clarify anything or if you have further questions.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

We invite you to give us your feedback on the UCSC Genome Browser
through May 31, 2007: http://www.surveymonkey.com/s.asp?U=881163743177




MI-KYUNG LEE wrote:
> To whom it may concern,
> 
> I have used Blat for my research. Thank you for the Blat.
> 
> By the way, I have questions for parameters of Blat. What does that mean
> minScore, minIdentity and minAli (for filtering  using pslReps)? How can I
> set those paremeters?
> 
> Your answer would be greatly appreciated.
> 
> Best regards,
> 
> Mi-Kyung from Texas A&M University
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome