Re: [Gusdev-gusdev] parseBlastFilesForSimilarity.pl

[Alberto D. <da...@io...>]

Basically we will use sequences (loaded into GUS with the GBParser) for
NCBI Blast (Blastx, Blastp and TBlastX), the same sequences will be also
used for Interpro analyses. Results of both (Blast and Interpro) will be
loaded into GUS. We will parse specific things from the Blast results, I
would say:

  `Gi` 
  `Accession` 
  `Description` 
  `E_value` 
  `Score` 
  `Length` 
  `Frame_Query` 
  `Frame_Hit` 
  `Identical` 
  `Hsp_Frac_Identical` 
  `Conserved` 
  `Hsp_Frac_Conserved`
  `Query_Start`
  `Query_End` 
  `Hit_Start` 
  `Hit_End` 
  `Hsp_Align` 
  `database_letters` 
  `database_entries` 

We already have a Bioperl parser for that (specific for another system:
GARSA) that could be adapted to GUS, problem being we are not sure what
tables should be used to store those data in GUS.

Cheers, Alberto


On Fri, 2005-02-11 at 10:06 -0500, Steve Fischer wrote:
> what are you planning on blasting?
> 
> steve
> 
> Alberto Davila wrote:
> 
> >Hi Steve,
> >
> >On Fri, 2005-02-11 at 08:56 -0500, Steve Fischer wrote:
> >  
> >
> >>poliana-
> >>
> >>oops, the usage statement for LoadBlastSimFast is out of date.   it 
> >>should instruct you to use the blastSimilarity command.
> >>
> >>LoadBlastSimFast makes a big assumption, that the subject and query 
> >>sequences are in GUS, and their def. lines have GUS primary keys. 
> >>
> >>Are your sequences already loaded into GUS?
> >>    
> >>
> >
> >They are not, there would be any howto/tips for that plugin ? We will
> >certainly need a plugin to load "Interpro" and "ORF finding" results
> >into GUS... If they are not available, then maybe we will have to write
> >them ...
> >
> >Cheers, Alberto
> >
> >  
> >
> >>steve
> >>
> >>
> >>
> >>Poliana Mateus wrote:
> >>
> >>    
> >>
> >>>Hello all,
> >>>
> >>>Where can find the script parseBlastFilesForSimilarity.pl??
> >>>I'm trying to run LoadBlastSimFast...
> >>>
> >>>Poliana