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

[Serge Gregorio]

Hello!  I'm not supposed to think about PHP for a week, 
much less write right now... but I just have to say my
THANKS to Frankie.  

Be back on Saturday... till then happy coding!

Cheers!

Serge

Frankie wrote:
 
---------------------------------------

On Sun, 18 May 2003 19:15:32  
 apu wrote:
>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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