Transeq

[Gary Williams, Tel 01223 494522]

You get the output in 'fasta' format by default.
If you want it in 'ncbi' format, then you have to ask for it:

transeq nucleic.seq ncbi::protein.pep 

or 

transeq nucleic.seq -osf ncbi protein.pep

Gary


Mick Watson wrote:
> 
> Hi
> 
> Can anyone tell me why when I give transeq a fasta file like:
> 
> >gnl|UG|Hs#S3220135
> ATGGCAGCGCGCCCGCTGCCCGTGTCCCCCGCCCGCGCCCTCCTGCTCGCCCTGGCCGGTGCTCTGCTCGCGCCCTGCGA
> 
> I get the output
> 
> >Hs#S3220135_1
> MAARPLPVSPARALLLALAGALLAPCEARGVSLWNEGRADEVVSASVRSGDLWIPVKSFD
> 
> Where has the "gnl|UG|" part of my description line gone???!!!  And
> why?  Can I switch this "feature" off?
> 
> Thanks
> Mick

-- 
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