[EMBOSS] Transeq and very large sequences
michael watson (IAH-C)
michael.watson at bbsrc.ac.uk
Mon Nov 27 15:47:17 UTC 2006
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
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
extension that may already help this for the next release.
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