Seq retrieval tool Announce

[Sebastian Bunka]

Dear EMBOSS users,

I'm using the EMBOSS program suite for a couple of months and I do not have
local/direct access to the embl/genbank databases. Since I wanted to use the
programs w/out every time downloading the embl/genbank entries by
search/click/save ... I have written a litte PERL program that can be easily
used by most emboss programs as a database/USA/app,external resource using
the NIH Entrez server. Maybe this program is useful for other people, too.

Links to the Homepage of gbwget and the project/download pages is at the end
of this email. I hope I did not waste your bandwith!

Thanks,
Sebastian


Announce:
gbwget is a nucleic/protein sequence search and retrieval program to be used
mainly by users of the EMBOSS sequence anylsis suite that do not have a
local access to the huge genbank, embl or swissprot sequence databases. It
allows users to directly use the (most ? of the) EMBOSS programs without
having to retrieve and store sequences manually through web interfaces. With
most programs of the EMBOSS suite one can give Uniform Sequence Addresses to
directly access database entries to perform different tasks. For instace to
quickly check for single restriction enzyme sites in one or more cloning
vectors (Example: pGEX-5x3 vector from Amersham/Pharmacia, genbank ID is in
the catalog) you only have to do: restrict -single ::gb:U13858 and you have
the list of enzymes. But only if you have direct access to the database.
Otherwise you have to open a webbrowser, go to http://www.ncbi.nlm.nih.gov,
choose nucleotide, search for U13858, save the data file, and the run
restrict on the file. And if you want to check the other 9 pGEX vectors ??
My program 'dbwget' enables EMBOSS users to do exactly that without local
access to the db's and much more. An alternative might be to install the SRS
program suite, but it's a quite large package and won't compile on linux (at
least for me and others).

I have written this program for me personally and use it now for my own
research in the field of molecular biology.

About:
gbwget is a command line/screen oriented tool to search in nucleotide
or protein databases and to view or retrieve database entries using
the Entrez server at http://www.ncbi.nlm.nih.gov. It is intended as
a sequence retrieval method for the EMBOSS (The European Molecular Biology
Open Software Suite, see:
http://www.uk.embnet.org/Software/EMBOSS/index.html) an alternative for
the gcg sequence analysis suite. gbwget can also be used standalone, but
web-based retrieval systems might be more comfortable.
LICENSE: GPL

Homepage and Download:
http://gbwget.sourceforge.net
and/or
http://sourceforge.net/projects/gbwget



Sebastian Bunka, Dr. med. vet.
Inst. Med. Chemistry, Vet. University Vienna
Ph. +43-1-250 77 ext. 4208, Fax: ext. 4290
e-mail: Sebastian.Bunka at vu-wien.ac.at