Re: [Gusdev-gusdev] parseBlastFilesForSimilarity.pl

[Steve F. <sfi...@pc...>]

luckily we are already adding that in 3.5

see AnalysisAlgorithm in the 3.5 roadmap: 
http://www.gusdb.org/wiki/index.php/Gus3.5RoadMap

steve

Josef Jurek wrote:

>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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