The eval 0.0e+00 and bit score 1481.0 both seem to be unlikely.
What version of BLAT are you using?
This could be a problem that has already been fixed.
>From kent/src/lib/blastOut.c
fprintf(f, "%3.1e\t", blastzScoreToNcbiExpectation(axt->score));
fprintf(f, "%d.0\n", blastzScoreToNcbiBits(axt->score));
static double blastzScoreToNcbiExpectation(int bzScore)
/* Convert blastz score to expectation in NCBI sense. */
{
double bits = bzScore * 0.0205;
double logProb = -bits*log(2);
return 3.0e9 * exp(logProb);
}
static int blastzScoreToNcbiBits(int bzScore)
/* Convert blastz score to bit score in NCBI sense. */
{
return round(bzScore * 0.0205);
}
>From kent/src/lib/axt.c
The function for calculating the axt->score
uses the blastz approach which has a simple
gapOpen/gapExtension scoring mechanism.
-Galt
On Fri, 9 Jan 2009, Mera Vigyan wrote:
> Good morning,
> I have a particular BLAT alignment in blast8 format like this :
>
> TOCA136B20FOR1 scaffold_24 99.87 773 0 1 1
> 772 4129889 4129117 0.0e+00 1481.0
>
> here the columns represent :
>
> Query id, Subject id, % identity, alignment length, mismatches, gap openings,
> q. start, q. end, s. start, s. end, e-value, bit score
>
> Here we have the alignment length as 773 with 1 gap. Then how come
> the score is given as 1481.
> What is the formula for score calculation in the "blast8" format ?
> kindly explain how this is done.
>
> warm regards
> Mera Vigyan
> _______________________________________________
> Genome maillist - [email protected]
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>
_______________________________________________
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