[Biophp-dev] [Biophp-dev]matrices scores (was:Re: levenshtein distance)

[biophp-dev@bioinformatics.org]

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Hello there,

first of all: sorry! i had some rather unpleasant real life stuff to
attend to, thats why i didnt write anything within a week.

Thursday, May 8, 2003, 9:17:22 PM, you wrote:

SG> Write a function that returns the SCORE based on the ff. matrix
SG> for example:
SG>    string A = "S  E  R  G  E"
SG>    string B = "F  R  A  N  K"
SG>               -2  0 -1  0  1 = -2 => FINAL SCORE
SG>[...]
D'oh! misunderstood the problem at first, this should be quite easy..

SG> Or you could use associative keys, e.g.
SG>    ( A => ( (A, 4), (R, -1), ... ) )
Did that since its easier for any function to access the values just
by doing matrix["A"]["Q"], then looking up indexes first.

SG> Of course, the next step is a function that handles strings of 
SG> unequal length, but we'll get to that later.
and alignment i guess. ill read myself through the website myabe i can
figure out some stuff ;)

attached is a bit of code that returns the score based on a matrix.
i  finished 2 matrices (blosum62 and PAM250) from the site you
referred to. but didnt check them for errors, yet.


-- 
Best regards,
 frank                            mailto:asseg@ukl.uni-freiburg.de
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