[Biodevelopers] Aminoacid charge

[Iddo Friedberg]

Hi Dinos,

Your question can be broken up into two: a substitution matrix 
describing protein sequences in terms of charges, and one that may be 
used by BLAST.

The former you can probably find looking to:
K Tomii and M Kanehisa  "Analysis of amino acid indices and mutation 
matrices for sequence comparison and structure prediction of proteins", 
Protein Engineering, 9(1):27-36   (1996)

http://protein.oupjournals.org/cgi/content/abstract/9/1/27

They describe a database of (then) 402 substitution matrices, publicly 
available over the web.Charge-related too.

For BLAST: this is a toughie. As far as I know, because of the heuristic 
nature in calculating the significance statistics, you cannot use a 
substitution matrix ontehr than those provided with BLAST (inc. their 
own gap insertion/extension penalties). You better talk to the BLAST 
help desk about that one.

I hope this helped,

Iddo



Konstantinos G. Liolios wrote:
> I want to compare proteins in terms of aminoacid charge instead of sequence.
> Where can I find an appropriatte substitution matrix for blast?  Any other
> ideas?
> 
> Dinos
> 
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-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
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http://bioinformatics.ljcrf.edu/~iddo