HyPhy message board | |
http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl
Datamonkey Server >> Datamonkey feedback >> Noncoding DNA http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1125611493 Message started by Jennifer Knies on Sep 1st, 2005 at 2:51pm |
Title: Noncoding DNA Post by Jennifer Knies on Sep 1st, 2005 at 2:51pm
I'd like to run Data Monkey on some non coding DNA in order to select the best fitting nucleotide substitution model. When I tried to do this, I received an error, alerting me to the prescence of stop codons in my sequence. Is there a way to tell Data Monkey that my sequences are non coding in order to accomplish my goal? Or do I have to try something else? Thanks!
|
Title: Re: Noncoding DNA Post by Sergei on Sep 1st, 2005 at 3:36pm
Dear Jennifer,
There are three things you can try (1). Run the model selection analysis on your machine using a HyPhy standard analysis. Choose Standard Analyses:Model Comparison:NucModelCompare.bf and use the following options for successive prompt - Global - Once - Choose Data file and tree - 0.0002 - choose a file to save results to (make a new directory to contain this file, because HyPhy will write out 203 files with a model fit for every model it tries). The best model will be printed at the end of the run (use the first printed model - it'll be the same one that Datamonkey would report). (2). Use the ciliate genetic code (only one stop codon there: TGA) if you only have TAA or TAG stop codons (3). Use a HyPhy standard analysis (Standard Analyses:DataFileTools:StripStopCodons.bf) to strip out stop codons before submitting to DataMonkey HTH, Sergei |
HyPhy message board » Powered by YaBB 2.5.2! YaBB Forum Software © 2000-2024. All Rights Reserved. |