[EMBOSS] Transeq and very large sequences

Peter Rice pmr at ebi.ac.uk
Mon Nov 27 15:15:25 UTC 2006

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.



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