[Biopython-dev] aaindex1

[Iddo Friedberg]

Brad Chapman wrote:


> Can we use Bio/AAIndex instead of AAIndex1? I'm not sure I really
> understand what the 1 signifies but it just seems a bit weird to me
> for no really good reason. Other than that, checking it in under
> there sounds great. If there's a good reason for using AAIndex1
> (like there is an AAIndex2 or something else) just tell me and do
> what you think it best.

AAIndex1 is a database (flat file) of 494 numeric values assigned to
amino acids. AAIndex2 are substitution matrices. I can create an AAIndex
directory, under which I will place the AAIndex1.py file. AAIndex2 will
have to wait.


> Oh yeah, and where is my documentation for Alphabet/Reduced.py? I'm
> gonna have to send my "documentation collection" agency out to see
> you pretty soon :-).

Egads! Not the dread DCA!!!

Just commited to CVS new versions of Bio.utils and Alphabet.Reduced it...

./I



-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 713 9930
http://ffas.ljcrf.edu/~iddo


-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 713 9930
http://ffas.ljcrf.edu/~iddo