[Bioperl-l] orientations and alignments

[Gregory Carl Kettler]

If I've created a SimpleAlign object by using, say, blast2seq on two DNA
sequences, is there a simple way to tell if one of the sequences is
reverse complemented in the alignment?  This is pretty easy to spot in the
blast output file (one sequence counts down), but I can't see any way
to get the information from a SimpleAlign object.

	Greg Kettler

"Of course, if you're writing the code to control a cruise missile, you
may not actually need an explicit loop exit.  The loop will be terminated
automatically at the appropriate moment."
	-Programming Perl, 3rd Ed.