[Biojava-l] SeqSimilaritySearchSubHit - Strand information
mark.schreiber at agresearch.co.nz
Tue Dec 2 15:04:04 EST 2003
Your right, this is confusing. It might be best to get the official answer from the ncbi blast help line:
blast-help at ncbi.nlm.nih.gov
If you could post their response to the list I think others may be interested.
> -----Original Message-----
> From: Jan Würthner [mailto:jan.wuerthner at uni-duesseldorf.de]
> Sent: Tuesday, 2 December 2003 9:52 p.m.
> To: biojava-l at biojava.org
> Subject: [Biojava-l] SeqSimilaritySearchSubHit - Strand information
> Hi folks,
> I'm constructing SeqSimilaritySearchSubHit instances from xml
> formatted NCBI
> BLAST results, and I'm getting steadily confused with the query's and
> subject's from and to information on one hand and the query's
> and subject's
> strand on the other hand.
> The NCBI returns for example:
> <Hsp_hit-frame> -1</Hsp_hit-frame>
> I'd think that the possibility to assign the from- and
> to-values in different
> orders (like descending in this query) already includes the
> information about
> the direction (POSITIVE/NEGATIVE). Why is there an additional
> "frame" value,
> and why is the query's frame value set to +1, and the
> subject's (=hit's)
> value set to -1? I assumed it to be assigned vice versa.
> My question is: How shall I set the SeqSimilaritySearchSubHit
> query/subject values from these data?
> Having answered this will be of much help!
> Thank you
> Jan Würthner
> Institute for Medical Microbiology
> Building 22.21
> Universitätsstraße 1
> 40225 Duesseldorf
> Tel. +49 (0) 211 81 12461
> URL: www.medmikro.uni-duesseldorf.de
> Biojava-l mailing list - Biojava-l at biojava.org
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