[EMBOSS] cutg database - Checked by AntiVir DEMO version -
gbottu at ben.vub.ac.be
Mon Jul 31 08:09:02 UTC 2006
On Fri, Jul 28, 2006 at 02:47:11PM -0500, Andres Pinzon wrote:
> On 7/28/06, Andres Pinzon <andrespinzon at gmail.com> wrote:
> > Is it necessary to dowwnload all gb* archives from
> > ftp://ftp.kazusa.or.jp/pub/codon/current/ in order to have the cutg
> > database running?
> It seems that one only need the CUTG.151.tar.gz (158Mb) file under the
> compressed/ directory. ;-)
> I have not ran the "cutgextract" command yet, i'll see.
It are actually the files *.codon that are needed for EMBOSS ;
downloading and extracting CUTG.151.tar.gz will do the job.
There is however a problem : cutgextract puts the files with codons in
.../share/EMBOSS/data/CODON. Under wEMBOSS this produces a selector with
thenthousands of entries, which causes delays in the transfer of the
Web page and is though to use. I do not know how EMBOSS explorer
behaves. The EMBOSS development team is considering putting the CUTG
files in a separate directory CUTG, but they have not yet done so. At the
BEN site I have modified cutgextract, so that it creates files with
extension .cutg instead of .cut ; wEMBOSS only displays the *.cut files
in the selector and the .cutg files can still be accessed by typing in
their name or by retrieving them with embossdata.
Hope this information helps,
Belgian EMBnet Node
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