[Biojava-l] SeqSimilaritySearchSubHit - Strand information

[Schreiber, Mark]

Hi -

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.

- Mark


> -----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_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
> 
> 
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