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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Fitting branch models with godon

Is it possible to fit branch models (Yang and Nielsen, 1998) in godon? That is, the model which averages over all sites, as opposed to the branch site models?
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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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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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1answer
29 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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1answer
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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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1answer
162 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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61 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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239 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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3answers
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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758 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 ...