[BiO BB] Re: BiO_Bulletin_Board Digest, Vol 4, Issue 8
milimetr at webmail.cmdik.pan.pl
Tue Feb 22 04:01:10 EST 2005
U can also try TESS:
with your own strings or matrix
dep. of Endocrinology
---------- Original Message -----------
From: bio_bulletin_board-request at bioinformatics.org
To: bio_bulletin_board at bioinformatics.org
Sent: Mon, 21 Feb 2005 12:34:21 -0500 (EST)
Subject: BiO_Bulletin_Board Digest, Vol 4, Issue 8
> Message: 3
> Date: Fri, 18 Feb 2005 15:13:20 +0100
> From: Yannick Wurm <Yannick.Wurm at unil.ch>
> Subject: [BiO BB] Refined Blast?
> To: bio_bulletin_board at bioinformatics.org
> Message-ID: <3E591300-81B7-11D9-A931-000D93712582 at unil.ch>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> for a specific need in my lab, we are looking for an implementation of
> nucleotide sequence alignment program which would be more flexible than
> standard BLAST.
> The reason is that we have sequenced dna fragments which have been
> submitted to chemical modifications which differentially affects
> different nucleotides.
> To help identify these sequences, we need to be able to fine-tune the
> matrix used for scoring. Thus, for example when calculating the "score"
> of an aligment, C->A and C->T could be given different weights.
> According to ebi.ac.uk, the WU-blast matrix is:
> A T G C
> A 5
> T -4 5
> G -4 -4 5
> C -4 -4 -4 5
> We want to be able to specifiy inidividual values to something like the
> following example:
> A T G C
> A 2
> T -4 8
> G -8 -10 3
> C -2 -1 -3 10
> To my surprise, BLAST does not have this liberty, despite the fact that
> different scoring matrices are used for proteins. I couldn't find
> anything on Google either.
> Would anyone one the list have a clue? Or do I need to get dirty
> messing with BLAST's source?
> Thanks in advance,
> . . . . . . . . . . . . . . . . . .
> yannick.wurm at unil.ch
> PhD student, Departement of Ecology and Evolution
> Université de Lausanne, Switzerland
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