Re: [Gusdev-gusdev] parseBlastFilesForSimilarity.pl

[<ju...@cs...>]

Concerning the DoTS.Similarity table which has been discussed
recently, what we at the Preuss lab are really hurting for
is a way to distinguish different Blast analyses (different
blast parameters) of the same subject and query sequences.
A table as simple as:

   id                             number(10)
   name                           varchar2(255)
   parameters                     varchar2(255)

so that one could store something as simple as:

   'Param Set 001'
   '-p blastx -M BLOSUM50 -G 13 -E 2 -e .01 -W 3'

and a way to link these entries to the rows of
DoTS.Similarity, perhaps in the way that
DoTS.NASequenceKeyword links rows of DoTS.NASequence
and DoTS.Keyword, would work.  If we were to go ahead and
add the table to the schema, we might want to actually
list the parameters individually with a
comment string, perhaps like:


   name                          varchar2(255)
   ...
   expectation_threshold         float(22)
   gap_penalty_existence         number(10)
   gap_penalty_extension         number(10)
   ...
   comment                       varchar2(255)

Are not other people on the list
missing the ability to distinguish
blast results by parameters?

Thanks, Josef



Josef Jurek, Ph.D.

Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

voice: (773) 834-3985
fax:   (773) 702-6648