HyPhy message board - Print Page

HyPhy message board
http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl Methodology Questions >> How to >> GARD and the reading frame http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1161113955 Message started by tlefebure on Oct 17^th, 2006 at 12:39pm

Title: GARD and the reading frame
Post by tlefebure on Oct 17^th, 2006 at 12:39pm

Hello,
When GARD splits the data but does not respect the reading frame, what should we do:
1. remove this codon
2. move the split upstream
3. move the split downstream

exemple:[code]
CHARSET span_1 = 1-940;
CHARSET span_2 = 941-1392;
CHARSET span_3 = 1393-1709;
CHARSET span_4 = 1710-2082;[/code]

The second fragment starts on position 2, and the third on position 3...

Thanks :P

Tristan

Title: Re: GARD and the reading frame
Post by Sergei on Oct 17^th, 2006 at 3:14pm

Dear Tristan,

GARD is nucleotide-based, hence it can't be expected to respect the reading frame. Generally speaking, you can probably move the breakpoints to the nearest codon boundary, or look at the support values for breakpoint locations output by GARD and move to the higher ones.

Cheers,
Sergei