Hi - Your right, this is confusing. It might be best to get the official answer from the ncbi blast help line:
[EMAIL PROTECTED] If you could post their response to the list I think others may be interested. - Mark > -----Original Message----- > From: Jan Würthner [mailto:[EMAIL PROTECTED] > Sent: Tuesday, 2 December 2003 9:52 p.m. > To: [EMAIL PROTECTED] > 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 > > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
