[Bioperl-l] BLAST scores

Joseph Bedell jbedell at oriongenomics.com
Thu Jun 30 17:48:36 EDT 2005

Hi Josh,

>-----Original Message-----
>From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l-
>bounces at portal.open-bio.org] On Behalf Of Josh Lauricha
>Sent: Thursday, June 30, 2005 4:03 PM
>To: bioperl-l at portal.open-bio.org
>Subject: [Bioperl-l] BLAST scores
>Not really a BioPerl question, but...
>I ran a bunch of blasts using the tablular output. However, I need the
>score reported and it apparently doesn't do that. The reason I'm using
>the tabular format is to speed parsing, since that was taking more than
>half the CPU time... Anyhow, is there anyway to compute the score from
>the e-value and/or bit scores? Or am I stuck rerunning all those
You can calculate the score given the bit score (from the tabular
output) and Lambda (calculated from the matrix). The equation is Score =
(Bits)/(Lambda in bits).

Lambda is only dependent upon the matrix. Did you use NCBI-blast or
WU-BLAST? Which flavor of blast (blastn, blastp, etc)? In any case, you
can just run a single blast and look at the stats at the bottom of the
report to get the value of lambda. For example, a default NCBI-blastn
(+1/-3) search has a lambda of 1.37

Lambda     K      H
    1.37    0.711     1.31 

Lambda     K      H
    1.37    0.711     1.31

But, what is difficult to discover is this lambda is in NATS. To convert
it to bits, divide it by the natural log of 2, or in perl:

perl -e 'print 1.37/log(2),"\n"'

So, now you can take all of your bit scores divided by 1.97649220601788
to get the Score.


>| Josh Lauricha            | Ford, you're turning    |
>| laurichj at bioinfo.ucr.edu | into a penguin. Stop    |
>| Bioinformatics, UCR      | it                      |
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