[BioC] BLAST E-value

[Richard Friedman]

Dear Alla,

	I am not acquainted with biostrings but the E value is not a function  
of a single alignment.
It is a function of an entire database search. It is the number of  
sequences in the database with the
same score or higher by chance.
Therefore there cannot be an E-value for a single pairwise
alignment. I can send you some instructional material from my course  
that deals with this issue off line if that would be helpful.

Best wishes,
Rich
------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

In Memoriam,
Patrick McGoohan



On Feb 16, 2010, at 1:36 PM, Alla Bulashevska wrote:

>
> 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.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor