hash function for 64 codons
gwilliam at hgmp.mrc.ac.uk
Tue Jun 19 05:23:00 EST 2001
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.
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
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