[Bioperl-l] retrieval of PRELIMINARY uniprot sequences using Bio::Registry fails

Daniel Lang daniel.lang at biologie.uni-freiburg.de
Fri Sep 1 06:11:58 EDT 2006


Hi,

when using Bio::Registry (bioperl-live) to fetch uniprot entries from
local indexed uniprot *.dats, I had to realize that several entries
could not be retrieved despite the fact that they are present in the
files! A closer look reveals that they are of status PRELIMINARY:

uniprot_trembl.dat:ID   Q16EZ1_AEDAE   PRELIMINARY;   PRT;   222 AA.

I don't "grep" PRELIMINARY anywhere in my cvs checkout..
I also can't retrieve the sequences from the online database defined as
follows:
[swissprot_ebi]
protocol=biofetch
location=http://www.ebi.ac.uk/cgi-bin/dbfetch
dbname=swall

Is this a bug or a feature? If its a feature, how can I bypass it?

Thanks in advance,
Daniel
-- 

Daniel Lang
University of Freiburg, Plant Biotechnology
Schaenzlestr. 1, D-79104 Freiburg
fax: +49 761 203 6945
phone: +49 761 203 6974
homepage:  http://www.plant-biotech.net/
e-mail: daniel.lang at biologie.uni-freiburg.de

#################################################
My software never has bugs.
It just develops random features.
#################################################





More information about the Bioperl-l mailing list