Hi Niels, Niels Larsen <[EMAIL PROTECTED]> 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. _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
