Welcome, Guest. Please Login
YaBB - Yet another Bulletin Board
 
  HomeHelpSearchLogin  
 
GARD (Read 1951 times)
Maria2
YaBB Newbies
*
Offline


Feed your monkey!

Posts: 2
GARD
Jul 19th, 2010 at 8:32am
 
Dear Datamonkeys
We have runned GARD to search for breakpoints in a set of 25 sequences (from a multigene family). But after re-running the program 10 times, we find back 1 or 2 breakpoints but at different sites. They do all fall in the same region, but how can we interpretate the data if it is not consistent? We want to use it for a PAML analysis to determine positive selection with the segmented regions, so how is the best way to proceede?. Could it be a problem with the alignment?
thanks in advance
Back to top
 
 
IP Logged
 
Sergei
YaBB Administrator
*****
Offline


Datamonkeys are forever...

Posts: 1658
UCSD
Gender: male
Re: GARD
Reply #1 - Jul 19th, 2010 at 5:19pm
 
Hi Maria,

GARD is a randomized algorithm -- it does always give the same answer. Are the breakpoints from the different runs fall within each others' confidence intervals? For instance, if run1 calls a breakpoint at 200, and the confidence interval is 150-250, and run2 calls a breakpoint at 180, then the results are not contradictor, but rather indicate lack of information content in the alignment.

PARRIS (implemented in datamonkey) is our implementation of partitioned selection analysis, but you should be able to do an analogous alignment (albeit with more programming and constant synonymous rates) in PAML.

Sergei
Back to top
 

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego
WWW WWW  
IP Logged