[Gusdev-gusdev] OrthoMCL procedure

[Arnaud K. <ax...@sa...>]

Hi everyone

To be able to reproduce the OrthoMCL method, I would like to raise two 
issues we've got:

* The first issue relates to the view where are stored the protein 
sequences. I was thinking to use the TranslatedAASequence view as this 
one contains the translated sequences of our gene models. The problem I 
have is that it is missing a name attribute so I can not match the blast 
output query and subject names with the data into GUS (I didn't want to 
use the TranslatedAASequence primary keys as the identifiers of my 
proteins of interest).
Could we add a name attribute to this view ?

* The second issue relates to the BLAST output parsing, done by a module 
called BlastAnal.pm in the CBIL package. This module seems to parse 
BLAST output file with only one query sequence. I have more than one 
query sequence reported so I had to change the code of this module to 
allow more than one query sequence. Can my code be integrated  to CBIL 
package ? Note that I didn't change the interface of this module so it 
doesn't affect the scripts that are using it, I'm thinking in particular 
of parseBlastFilesForSimilarity.pl

cheers
Arnaud