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

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

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 have=20
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 plugins.=20
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 wha=
t
>LoadNRDB is doing-- specifically how it handles the gitax file.  We 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 informat=
ion.
>
>--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,=20
>>
>>=20
>>
>>We=B9re trying to insert a Blast result into Gus Schema using LoadNRDB
>>plug-in. Our blast result was filtered and is in a Fasta format accordi=
ng to
>>the plug-in requirement. The problem is the load process takes many tim=
es
>>and our postgres server process crashes after some hours, thus the plug=
-in
>>never concludes. I would like to know why this plug-in is so slow, if t=
he
>>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.
>>
>>=20
>>
>>Does anyone could help us to understand this?
>>
>>=20
>>
>>Thanks a lot,
>>
>>=20
>>
>>Fabr=EDcio.
>>
>>   =20
>>
>
>------ End of Forwarded Message
> =20
>