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GARD and the reading frame (Read 1769 times)
tlefebure
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Cornell University
GARD and the reading frame
Oct 17th, 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; 



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

Thanks  Tongue

Tristan
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Sergei
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UCSD
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Re: GARD and the reading frame
Reply #1 - Oct 17th, 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
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