Re: [Gusdev-gusdev] parseBlastFilesForSimilarity.pl

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

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oops, the usage statement for LoadBlastSimFast is out of date.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
>>>>>          
>>>>>
>
>  
>