[BiO BB] Determining gap penalties & bits

Iddo Friedberg idoerg at cc.huji.ac.il
Thu May 31 06:36:31 EDT 2001

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?




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                                          |

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