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

[Jonathan C. <cra...@pc...>]

Michael-

MICHAEL LUCHTAN wrote:
> 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?

 From what I recall, the terms "query" and "subject" are taken from the wording
used in WU-BLAST output.  The query sequence is the sequence with which you are
BLASTing, and a subject sequence is one of the sequences hit/found by the BLAST
search.  Other people use different terms for these concepts (e.g., "target"
sequence instead of subject sequence) but the idea is the same.  The Similarity
table is designed to store pairwise alignments, and in the case where those
alignments are the result of a search (e.g. BLAST), you want to be able to
distinguish the query sequence from the subject/database/target sequences.  The
only added complication in GUS is that many of the references in the database
use both a table_id (to identify the table being referenced) and also a row_id
(to identify the specific row.)  The table_ids are just foreign keys into the
core.TableInfo table, which lists all of the tables in the database.

In your particular example, the query_table is DoTS.ExternalNASequence, because
that's the table from which you extracted your BLAST query sequence.  I don't
know what your subject_table will be, because I don't think you mentioned what
database you were BLASTing against.  An important thing to note is that the
plugin that loads BLAST similarities requires that all the sequences involved
be in the database already.  So if you were BLASTing against SWISS-PROT, for
example, you would first make sure that the relevant entries from SWISS-PROT
(or, to simplify matters, all of them) had been loaded into the
DoTS.ExternalAASequence table (which would then serve as your subject table.)
For a BLAST search against ProDom or CDD, you'd likely be using the MotifAASequence
table (actually a view) instead.  Let me know if this doesn't make sense,

Jonathan