[BioC] BLAST E-value

[michael watson (IAH-C)]

http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/bl2seq.html

This does indeed provide a BLAST e-value.
________________________________________
From: bioconductor-bounces at stat.math.ethz.ch [bioconductor-bounces at stat.math.ethz.ch] On Behalf Of michael watson (IAH-C) [michael.watson at bbsrc.ac.uk]
Sent: 17 February 2010 22:44
To: Alla Bulashevska; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] BLAST E-value

Have you tried the bl2seq program from NCBI?
________________________________________
From: bioconductor-bounces at stat.math.ethz.ch [bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Alla Bulashevska [alla.bullashevska at fdm.uni-freiburg.de]
Sent: 16 February 2010 18:36
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] BLAST E-value

Dear Bioconductor users,
i am doing cross-species analysis and searching for the way
how to pairwise align thousands of sequences efficiently. I
should become the BLAST E-value as output.
The pairwiseAlignment in the Biostrings package can align
 two protein sequences but outputs Smith Watermann score.
I will appreciate it greatly if somebody can tell me, how
this score could be transferred into E-value.

Thank you for your help,
Alla.

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