Transeq

[Mick Watson]

OK, thanks for the help!

In this instance I really wanted the first part of the fasta line to stay the
same - I realise that it doesn't anyway die to the "_1" which is appended -
so now as well as removing that I am also putting the "gnl|UG|" part back on
the front too!

My first instinct would be to just leave the fasta line alone other than to
simply append _# to the translation......

Peter Rice wrote:

> "Gary Williams, Tel 01223 494522" wrote:
> >
> > 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
>
> You still lose the "UG" database name. You wil get an identifier of:
>
> >gnl|unk|Hs#S3220135_1
> MAARPLPVSPARALLLALAGALLAPCX
>
> NCBI's "FASTA" identifiers are strange things that EMBOSS can read but not
> save completely ... but this should not be a problem because "UG" is not
> really the database name for the protein translation.
>
> Peter
>
> --
> ------------------------------------------------
> Peter Rice, LION Bioscience Ltd, Cambridge, UK
> peter.rice at uk.lionbioscience.com +44 1223 224723