Re: [Gusdev-gusdev] parseBlastFilesForSimilarity.pl

[Y. T. G. <yon...@pc...>]

Hi Alberto:
When doing similarity analyses (BLASTs, BLAT) with GUS, here is the
process we usually follow:

1: load query sequence set into GUS if not already in GUS (will get a GUS
id for each sequence); same for target sequence set
2: dump from gus to get query fasta file and target fasta file using the
script $GUS_HOME/bin/dumpSequencesFromTable.pl
3: run blast on computer cluster using the DistribJob software
4: run load plugin to load result into similarity table 
(DoTS.BlastSimilarity for BLAST, DoTS.BLATAlignment for BLAT alignments)

In your case, I think you will need to load NR, NT as separate datasets 
into GUS (EST should already be in GUS)

-Thomas

On Fri, 11 Feb 2005, Alberto Davila wrote:

> All the blastable databases I mentioned are standard databases from NCBI
> (ftp://ftp.ncbi.nlm.nih.gov/blast/db/blastdb.txt):
>
> NT = nucleotides
>
> ~30000 entries from genbank (genbank format) are loaded into GUS now.
>
> Not sure about your "NRDB", I know NR from NCBI that is a collection of
> aminoacid entries, could it be the same ?
>
> Alberto
>
> On Fri, 2005-02-11 at 10:43 -0500, Steve Fischer wrote:
>> (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
>
>
>
>
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