hash function for 64 codons

[Gary Williams]

In article <kOm*dROYo at news.chiark.greenend.org.uk>,
Tim Cutts <timc at chiark.greenend.org.uk> wrote:
>In article <etdvglzf04l.fsf at lola-granola.mit.edu>,
>Alex  <new_name at mit.edu> wrote:
>>
>>> I guess there is probably a good hash function out there that hashes
>>> the 64 codons, which I assume is the fastest way to do translation.
>>
>>I think a 4x4x4 lookup table is faster, actually.
>
>I agree.  I have some C code which uses this method (in fact, two 4x4x4
>tables) to translate all six reading frames in a single pass over the
>input DNA sequence (no reverse complementation step is therefore
>necessary).  I think it's pretty much as fast as I can make it.

I use a 15 x 15 x 15 3D array in the translation routines in EMBOSS.

I've passed Bin Li some of my code from EMBOSS.

See: 
 
http://www.hgmp.mrc.ac.uk/Software/EMBOSS/

http://srs.hgmp.mrc.ac.uk/srs6bin/cgi-bin/wgetz?-id+2kdrv1G_ugd+[edata-ID:AjPTrn]+-e

Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
mailto:G.Williams at hgmp.mrc.ac.uk            http://www.hgmp.mrc.ac.uk/
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK