[EMBOSS] Transeq and very large sequences

[michael watson (IAH-C)]

Hi Peter

Yes, a 6-frame translation of a chromosome :)  It was meant to be part
of a quick-and-dirty analysis method, but is proving to be anything but
quick....

Mick 

-----Original Message-----
From: Peter Rice [mailto:pmr at ebi.ac.uk] 
Sent: 27 November 2006 15:15
To: michael watson (IAH-C)
Cc: emboss at lists.open-bio.org
Subject: Re: [EMBOSS] Transeq and very large sequences

michael watson (IAH-C) wrote:

> I want to translate very large (eukrayotic chromosomes!) DNA sequences
> in all 6 frames.  Transeq takes about a day per large chromosome,
> running on a linux machine with 3Gb of RAM. 
> 
> Any suggestions on alternatives or how I could speed it up?

You want just a 6-frame translation of an entire chromosome?

I will look into why it takes so long. We have made some changes to
string size 
extension that may already help this for the next release.

regards,

Peter