FASTA glitch.

pmiguel at bilbo.bio.purdue.edu pmiguel at bilbo.bio.purdue.edu
Mon Apr 25 14:52:50 EST 1994

  (This is about the version of FASTA in GCG.)
  When a DNA FASTA search displays an alignment in which the query is /REV 
(i.e., reverse complement, i.e., bottom strand) it numbers it incorrectly.  
That is, the last base of the sequence becomes "1", the next to the last 
"2" and so on.  Why hasn't this been fixed over the years?  BESTFIT, for 
example, doesn't do this.  Why doesn't FASTA display reverse alignments 
like BESTFIT?  What would it take, an extra 10 lines of code?  It drives me 
nuts every time I have to do it by hand!


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