[EMBOSS] Antwort: Genbank GI fetching?

[david.bauer at bayerhealthcare.com]

Hi Niels,

Niels Larsen <niels at genomics.dk> schrieb am 15/06/2007 18:32:13:

> http://emboss.sourceforge.net/apps/release/4.1/emboss/apps/groups.html
>
> and click about, hunting for seqret, but dont find (I wanted

you could find seqret in the edit group but unfortunately this belongs to
the category "broken link".

> Finally question: I will build an accessor (in Perl) that
> invokes seqret for pulling out a genbank sub-sequence, often
> just a small piece, plus the features that overlap with this
> piece. Can EMBOSS do this, or must I pull the whole entry,
> parse and find the overlapping pieces in Perl?

There are (at least) 3 programs in EMBOSS which could be helpfull for this
task:
1) showfeat
Returns a nice parsable overview of the features in the GenBank entry.
2) extractfeat
Extracts sequence of features from the GenBank entry.
3) coderet
This is for mRNA and CDS features and takes care of joining the exons and
get the protein sequence of a CDS.

Cheers,
David.