Re: [Gusdev-gusdev] parseBlastFilesForSimilarity.pl

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

Query:

Either sequences from genbank (genbank format) or sequences generated in
the lab (fasta format)

Blastable databases (all are formatted databases from NCBI):

NR
NT
EST

Alberto

On Fri, 2005-02-11 at 10:34 -0500, Steve Fischer wrote:
> for the blast, what are the query sequences and what are the blastable 
> databases?
> 
> steve
> 
> Alberto Davila wrote:
> 
> >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oops, the usage statement for LoadBlastSimFast is out of date.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