[Gmod-help] Re: [Gmod-gbrowse] questions about sequence strand orientation and problem in show_mismatch

[Don Gilbert]

Dave is right in that by common practice if not formal definition, the
Target strand is usually positive, since you are dealing with a match 
of two sequences that, usually, don't have an intrinsic orientation. 

However, GFF3 format specification does provide for - Targets
http://song.sourceforge.net/gff3.shtml
ctg123 . EST_match  2000 2500 . + . ID=match002;Target=EST_B 1 500 -
"The strand field in column #7 is "+" indicating that the match is to a
transcript feature on the forward of the genome.  The strand field in
the Target attribute is -, indicating that the EST sequence should be
reverse complemented in order to align to the underlying transcript."

I don't know if the problem you see indicates a Gbrowse mistake in
handling GFF Targets or not. Is your data display correct if you factor
in reverse-complementation?

-- Don