[EMBOSS] cutg database - Checked by AntiVir DEMO version -

Guy Bottu 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.

	Dear Andres,

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,
	Guy Bottu,
	Belgian EMBnet Node

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