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How to make a correct Codon Usage bias??? (Read 3060 times)

jackson YaBB Newbies Offline I love YaBB 1G - SP1! Posts: 30 São Paulo, Brazil Gender:	How to make a correct Codon Usage bias??? Feb 26^th, 2007 at 10:24am Hello HYPHY team, I'm Jackson from Brazil and I work with phyogenetic analysis of rotavirus. I want to make the Codon Usage Bias, but i'm not sure how to use and how to make this analisys. The CodonUsageBias.bf of HYPHY is appropriate to do this? Thanks your attetion. Jackson Lima
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Sergei

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Datamonkeys are forever...

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Re: How to make a correct Codon Usage bias???
Reply #1 - Feb 26^th, 2007 at 5:24pm

Dear Jackson,

Are you trying to estimate one of the standard measures (like CAI - codon adapatation index)?

The file you cite is an exprimental analyses that attempts to identify codon sites in an alignment which have codon usage significantly different from the background (data set average).

Cheers,
Sergei

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

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jackson YaBB Newbies Offline I love YaBB 1G - SP1! Posts: 30 São Paulo, Brazil Gender:	Re: How to make a correct Codon Usage bias??? Reply #2 - Feb 27^th, 2007 at 6:19am Dear Sergei, Yes, like CAI, CBI and RSCU. If HYPHY can't make, do you recommend any software? Sorry about the newbie questions... ??? Cheers, Jackson
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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: How to make a correct Codon Usage bias??? Reply #3 - Feb 28^th, 2007 at 10:09am Dear Jackson, I have some batch files for CAI and other measures in my archives; let me dig them up and post the links. Cheers, Sergei
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jackson YaBB Newbies Offline I love YaBB 1G - SP1! Posts: 30 São Paulo, Brazil Gender:	Re: How to make a correct Codon Usage bias??? Reply #4 - Mar 16^th, 2007 at 11:18am Ok Sergei. I'll be waiting your batchfiles for make the tests.
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