[BiO BB] Re: BiO_Bulletin_Board Digest, Vol 4, Issue 8

[MACIEJ PIETRZAK]

Hi,

U can also try TESS:
http://www.cbil.upenn.edu/tess/

with your own strings or matrix 

Regards

Maciej Pietrzak
dep. of Endocrinology
MRC PAS 
WARSAW, POLAND
milimetr<at>cmdik.pan.pl

---------- 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
> 
> Hi,
> 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
> 
> . . . . . . . . . . . . . . . . . .
> yannick.wurm at unil.ch
> +41.21.692.4157
> PhD student, Departement of Ecology and Evolution
> Université de Lausanne, Switzerland
>