[Bio-Linux] New Partigene and Trace2dbest packages on Bio-Linux

Bela Tiwari btiwari at ceh.ac.uk
Tue Jun 26 08:13:21 EDT 2007


Hello all, 

This is just to let you know that the bio-linux-trace2dbest and bio-linux-partigene packages have been updated on the server. The versions now available are 3.01 and 3.03 respectively.

There are onlya couple of small changes in the bio-linux packages relative to the original distributions: 
    -The maximum length for a blast database name has been changed from under 10 to under 20 characters. 
    - The version of CLOBB installed can take in files with endings of .fsa or .fasta. 

In addition, there is a file called PartiGene_predb.pl_modified in /usr/local/bioinf/partigene/partigene.  This file contains an ugly, and only partially effective,  hack to get around a problem that sometimes (!), arises due to the names given to blast report files. 
Please see the information in /usr/local/bioinf/partigene/partigene/readme.biolinux  for further details after the upgraded packages are installed. By default, PartiGene_predb.pl_modified is not set up to run; it is only any use if you are generating html pages and run into this issue with blast report names. We have contacted the partigene developers about this issue.


cheers,

Bela 

*************************
Dr. Bela Tiwari
Lead Bioinformatician
NERC Environmental 
Bioinformatics Centre

CEH Oxford
Mansfield Road
Oxford, OX1 3SR
01865 281975

*************************






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