(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!