[Gusdev-gusdev] Questions about LoadBlastSimFast.pm

[Jeetendra S. <so...@vb...>]

Hi,

1. Does anyone know how do I link the Similarity tables (Dots.similarity
and Dots.similarityspan) with the ExternalAASequence (or
ExternalNASequence) table ?
     Let's assume that we already have the query and subject sequences in
ExternalAASequence, and the BLAST results in the similarity tables.
Now, using the similarity tables, I can only get query_table_id and
subject_table_id, and not the actual sequence_id. However, I want to
access the actual query and subject sequences. After accessing the
Similarity.min_query_start and Similarity.max_query_end values, how
do I access the actual query sequence, since there might be a large
number of sequences in the table referred by query_table_id?

2. Since the Similarity.algorithm_id value is not a part of the parsed
Blast output generated by generateBlastSimilarity.pl, what is the best way
to incorporate algorithm information in Dots.Similarity ?

Thanks,
Jeetendra.

-- 
Jeetendra Soneja
Research Associate
Virginia Bioinformatics Institute
1880 Pratt Dr., Building XV
Blacksburg, VA 24060, USA
Phone: (540)-231-2789
http://www.vbi.vt.edu