Re: [Gusdev-gusdev] parseBlastFilesForSimilarity.pl

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

(what is NT?)

which of these (genbank, your fasta, NRDB, NT, EST) have you loaded into 
gus?

steve

Alberto Davila wrote:

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oops, the usage statement for LoadBlastSimFast is out of date.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