[EMBOSS] Transeq and very large sequences

[Peter Rice]

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