Re: [Gusdev-gusdev] OrthoMCL procedure

[Steve F. <sfi...@pc...>]

Arnaud-

see below.

steve

Arnaud Kerhornou wrote:

> 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 ?

hmm.   not quite following.   what would this name be, where would it be 
derived from?   why not use source_id and/or secondary_identifier?    
or, presumably this translated sequence has a relationship back to its 
na sequence (although i don't immediately see that in the schema 
browser), so couldn't you get a name or source_id from there?

>
> * 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

this sounds ok.   how about we just take a quick look at this together 
while you are visiting?   then we can fold it into the code base.   do 
you want to send it by mail?

>
> cheers
> Arnaud
>
>
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