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FASTA glitch.

Tim Bolling bollingt at ugene1.abbott.com
Tue Apr 26 13:10:13 EST 1994


>   The situation is even more confusing if I'm restricting the database 
> search to a sub-section of my sequence -- say 200 to 600.  If I get a /rev 
> hit (a hit on the reverse complement strand) from 300 to 350 according to 
> fasta, the real region of homology will be from 500 to 450!  It took me 
~
~

So what you are saying is that the numbering should be absolute based on the
original orientation and numbering of the query sequence, right?  Thus, 
homology in nt pos. 200-350 would be so indicated regardless of which 
orientation matches or what region was specified.  That makes sense.  Just to
give GCG the benefit of the doubt, I think that they probably don't consider
this a "bug" because they haven't been approached with a united front 
regarding the "best" numbering scheme.  There are probably those who have
gotten used to the current numbering and might be resistant to change.  If,
however, you are saying what I think you are saying, then I'm in total 
agreement with your suggestion. 



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