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

[CHAN, KENNETH 1 [AG/7721]]

Thanks Dave and Don for clarifying.
Yeah, the reverse-complement works fine in gbrowse.
I was trying to display the contigs alignments but some contigs were not
in a correct orientation in the Fasta file (only reverse, not
reverse-complement). Since gbrowse does not provide the only reverse,
and only complementation manipulation. For a work around, I reversed the
sequence in the FASTA file before applying to gbrowse. Anyway, thanks
for clarifying and confirming this.

Regards,
Kenneth



-----Original Message-----
From: Don Gilbert [mailto:gilbertd at cricket.bio.indiana.edu] 
Sent: Saturday, March 06, 2010 7:24 AM
To: help at gmod.org; CHAN, KENNETH 1 [AG/7721]
Cc: gmod-gbrowse at lists.sourceforge.net
Subject: Re: [Gmod-gbrowse] questions about sequence strand orientation
and problem in show_mismatch

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


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