Re: [Gusdev-gusdev] parseBlastFilesForSimilarity.pl

[Ed R. <ero...@ug...>]

We need to store much more information in general about
algorithm implementations.  Even more than parameters, we need
information on training sets used, etc.  The existing
algorithm and algorithmimplementation table do not provide
enough detail.  Worse, some tables connect to them backwards.
   Dots.SignalPeptideFeature has a FK link to core.algorithm,
not to core.algorithmimplementation, which means there is no
way to associate a run of signalP with a version of (1, 2, or 3?).

-ed



---- Original message ----
>Date: Thu, 17 Feb 2005 14:55:16 -0600 (CST)
>From: ju...@cs..., Josef Jurek
<ju...@cs...>  
>Subject: Re: [Gusdev-gusdev] parseBlastFilesForSimilarity.pl  
>To: gus...@li...
>Cc: 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
>
>
>
>
>
>
>
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-----------------
Ed Robinson
Center for Tropical and Emerging Global Diseases
University of Georgia, Athens, GA 30602
ero...@ug.../(706)542.1447/254.8883