Re: [Gusdev-gusdev] format of sequences for blast

[MICHAEL L. <lu...@cs...>]

Hello --

I used the following script to get some data out of GUS:
#!/usr/bin/perl

use GUS::ObjRelP::DbiDatabase;
use GUS::Common::GusConfig;

my $gusconfig=
GUS::Common::GusConfig->new("/home/luchtan/gus.properties");
my $db= GUS::ObjRelP::DbiDatabase->new($gusconfig->getDbiDsn(),

$gusconfig->getReadOnlyDatabaseLogin(),

$gusconfig->getReadOnlyDatabasePassword,
                                        1,1,1,
                                        $gusconfig->getCoreSchemaName);
my $dbh= $db->getQueryHandle();

my $idStmt= $dbh->prepare("select '>'||na_sequence_id||' '||name||'\n'
name_str,sequence from dots.externalnasequence");
$idStmt->execute();
open(TEMP, ">retrievedSeqForBLAST.tmp");
while(my (@row)=$idStmt->fetchrow_array()){
    print TEMP "@row\n";
}
close(TEMP);


and blasted the resulting retrievedSeqForBLAST file.  Now I want to load
the results into GUS using the plugin LoadBlastSimilaritiesPK.
This plugin requires a subject_table and a query_table.  Perhaps it is a
question of my unfamiliarity of the whole biology aspect of what is going
on here(I'm just a programmer), but I am not sure what these tables are
for.  Can anybody help me
out?

Michael Luchtan
http://www.cs.uga.edu/~luchtan


On Thu, 22 May 2003, Jonathan Crabtree wrote:

>
> Jessie-
>
> Jessica Kissinger wrote:
> >     If memory serves me correct, once sequences were loaded into GUS, we
> > then retrieved them along with their GUS ID to submit for blast searches.
>
> Yes, I think that's right.
>
> >     When we retrieved the sequences, we created a custom format for the
> > header line, such that the blast results once generated for these
> > sequences could be easily parsed and loaded with the existing plug-in.
> >
> >     Can someone tell me what the format of the fasta header should be,
> > i.e is it ">GUSID, External_NA _sequence Name" or the other way around
> > and should there be any formatting, tabs, spaces etc.  If I remember
> > correctly, the blast results were loaded by GUSID not "name", but I
> > don't remember.
>
> My recollection is that the defline started as you said, with ">GUSID ".
> I don't believe that the format is crucial, because (again, from what
> I remember) when you run the plugin to load the BLAST similarities you
> supply it with a regular expression that it uses to pick the GUSID
> (an na_sequence_id for most of the PlasmoDB searches) out of the defline.
> So as long as the regex matches the defline format, you should be OK,
> and I don't think that the plugin uses anything on the defline except
> for the GUSID.
>
> Jonathan
>
>
>
>
>
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