[BiO BB] Determining gap penalties & bits

Mr M senthil kumar senthil at www.cdfd.org.in
Thu May 31 21:48:23 EDT 2001


Hi Friedberg,
   I think Emboss has a program called water which does the Smith-Waterman
algorithm. More can be found at 
http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/water.html
Hope this helps, 
Senthil Kumar M.

--
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# Senthil Kumar M.                            #
# Junior Research Fellow,                     #
# Center for DNA fingerprinting & Diagnostics,#
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On Thu, 31 May 2001, Iddo Friedberg wrote:

> Hi all,
> 
> A question regarding scoring matrices follows:
> 
> 
> Is there some formal way to determine gap penalties for the Smith-Waterman
> algorithm given a log-odds scoring matrix? I know GCG/Wisconsin package
> does something, but I could not find any documentation on that. Also, how
> do I determine the best number of bits in which to represent my scoring
> matrix? That is, what are good values for N in the function:
> 
> N*log(Pij/Pi*Pj)    (log in base 2)
> 
> which is a matrix entry?
> 
> Pij: frequency of substitutions between amino-acid j and amino-acid i
> Pi,Pj: frequencies of amino-acids i and j, respectively.
> 
> Any pointers to relevant literature?
> 
> Thanx,
> 
> Iddo
> 
> --
> 
> Iddo Friedberg                                  | Tel: +972-2-6758647
> Dept. of Molecular Genetics and Biotechnology   | Fax: +972-2-6757308
> The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il
> POB 12272, Jerusalem 91120                      |
> Israel                                          |
> http://bioinfo.md.huji.ac.il/marg/people-home/iddo/
> 
> 
> 
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