[Biojava-l] SeqSimilaritySearchSubHit - Strand information

[Jan Würthner]

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_query-from>576</Hsp_query-from>
       <Hsp_query-to>229</Hsp_query-to>
       <Hsp_query-frame>1</Hsp_query-frame>

       <Hsp_hit-from>12374053</Hsp_hit-from>
       <Hsp_hit-to>12374401</Hsp_hit-to>
       <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 instance's 
query/subject values from these data?

Having answered this will be of much help!

Thank you
Jan

-- 
Jan Würthner
Institute for Medical Microbiology
Building 22.21
Heinrich-Heine-University
Universitätsstraße 1
40225 Duesseldorf

Tel. +49 (0) 211 81 12461
URL: www.medmikro.uni-duesseldorf.de