[Bioperl-l] BLAST scores

[Josh Lauricha]

On Thu 06/30/05 16:48, Joseph Bedell wrote:
> 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 
> 
> Gapped
> 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"'
> 1.97649220601788
> 
> So, now you can take all of your bit scores divided by 1.97649220601788
> to get the Score.
> 
> HTH,
> Joey

Cool, thanks. That'll save me a bunch of time ;) This was NCBI blastp,
so I've already got it calculated ;)

Thanks.

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