Re: FW: [GUSDEV] Load a Blast result using LoadNRDB

[Deborah P. <pi...@pc...>]

I reread your e-mail and am guessing that your file is a file of=20
sequences (query or subject ?) with information on the defline=20
pertaining to a BLAST analysis. Perhaps you can send an excerpt of your=20
file  and a bit more explanation. Perhaps we can make some better=20
suggestions.

                                                                         =
                                   =20
Debbie



Deborah Pinney wrote:

> LoadNRDB.pm is not the appropriate plugin to use to load BLAST results=20
> into GUS. It is specifically designed to load defline and sequence=20
> information  from NCBI's non redundant protein database files. It uses=20
> the gitax file to get taxon information for each of the gi numbers in=20
> the defline so as to attach a taxon_id. Therefore, LoadTaxon would=20
> have to be run with NCBI's taxonomy files prior to running LoadNRDB.
>
> There is at least one plugin that can be used to load BLAST results,=20
> InsertBlastSimilarities.pm, which is one of the GUS/Supporterd=20
> plugins. Take a look at that and see if it serves your purposes.
>                                                                        =
                                                                         =
   =20
> Debbie
>
>                                                 =20
>
>
>
> Michael Saffitz wrote:
>
>> Hi Debbie,
>>
>> Can you help with this?  I think we should start with an overview of=20
>> what
>> LoadNRDB is doing-- specifically how it handles the gitax file.  We=20
>> can then
>> figure out if Fabricio's issue is in the data or code.
>>
>> Please include gusdev in your reply-- I think it will be useful=20
>> information.
>>
>> --Mike
>>
>> ------ Forwarded Message
>> =20
>>
>>> From: Fabr=EDcio <fab...@de...>
>>> Date: Thu, 9 Jun 2005 16:38:44 -0300
>>> To: <gus...@li...>
>>> Subject: [GUSDEV] Load a Blast result using LoadNRDB
>>>
>>> Hello all,
>>>
>>>
>>> We=B9re trying to insert a Blast result into Gus Schema using LoadNRD=
B
>>> plug-in. Our blast result was filtered and is in a Fasta format=20
>>> according to
>>> the plug-in requirement. The problem is the load process takes many=20
>>> times
>>> and our postgres server process crashes after some hours, thus the=20
>>> plug-in
>>> never concludes. I would like to know why this plug-in is so slow,=20
>>> if the
>>> file we want to store is not so big. I think that it=B9s due to the
>>> =ADgitax=3Dgi_taxid_prot.dmp parameter that has a large file.
>>>
>>>
>>>
>>> Does anyone could help us to understand this?
>>>
>>>
>>>
>>> Thanks a lot,
>>>
>>>
>>>
>>> Fabr=EDcio.
>>>
>>>  =20
>>
>>
>> ------ End of Forwarded Message
>> =20
>>
>
>
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