Questions tagged [codon]

A sequence of 3 DNA or RNA bases coding for an amino acid or a stop signal. Codons are read in the ribosome to synthesise proteins using the tRNA, which are the link between each codon and the corresponding amino acid/stop signal. Codons can have different meanings depending on the organism.

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Are there other currently available codon bias indexes , other than Kaks, to distinguish between positive and negative selection?

I am currently dealing with the study of T.gondii's proteome. I downloaded the complete set of CDS from NCBI GenBank and I am now starting to decide how to implement the analysis. I'm pretty ...
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156 views

Are codons in RNA layered? Are we misinterpreting RNA codons?

I am analyzing nucleotide base-pair patterns in RNA and DNA, and had a thought about RNA and DNA (Let me first state though, I am not a biologist; I am an algorithmatician, employing a sort of ...
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26 views

panic: division of zero by zero or infinity by infinity error when running GODON positive selection analysis

I am using godon to find genes under positive selection with the branch-site test. However, after running for a little while I get the error "panic: division ...
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What are the p01sum and p0prop parameters in godon?

When using branch-site model in Godon, model optimization results include the following parameters: p01sum and p0prop. What are ...
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145 views

Pipeline for extracting gene from multiple genomes for use in HyPhy selection analyses?

I have been trying to obtain some preliminary data from HyPhy selection analyses to inform a larger project. I have obtained a number of assembled mammalian genomes from NCBI with the initial goal of ...
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58 views

Codon usage analysis for whole genomes

I am new to bioinformatics. So if these questions seem you to a bit childish please forgive me. I have two queries. I am intending to perform a codon usage analysis followed by correspondence ...
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194 views

How can I calculate the silent mutation for each position in codon?

I am trying to find the number of silent mutations in for each position in codon. In the homework, I am asked: For the codons and for each position, count the number of silent mutation. There are ...
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2k views

Which sequence alignment tools support codon alignment?

Sometimes it useful to perform a nucleotide protein coding gene sequence alignment based on codons, not on individual nucleotides. For example for further codon model analysis it is important to have ...
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683 views

How to run HYPHY on multiple files non-interactively?

I would like to test for positive selection in a large set of genes. I want to have a yes/no answer to the question if gene was evolving under positive selection. Therefore I chose model BUSTED for ...