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.

Filter by
Sorted by
Tagged with
1 vote
1 answer

Pal2nal translation of large multi-fasta files produces a codon translated file where some sequences half length of the average

I did sequence alignment of a large peptide multi-fasta (n= 4991 sequences). The peptide alignment has sequences with the same length and pal2nal went through just fine... except some of the codon ...
Sudoh's user avatar
  • 217
3 votes
1 answer

Find a genomic coordinates for a protein aminoacid position

Is there a function that can map genomic position (hg19) back from a protein position? I can have name of a particular transcript, and exon number. For example, I have KRAS gene for which I would like ...
lizaveta's user avatar
  • 203
2 votes
2 answers

Bacterial genomes and snpeff warnings 'WARNING_TRANSCRIPT_NO_START_CODON'

I annotated a bunch of genomes with snpeff. And although the original reads' qualities and the matches with the reference genomes were quite high, I see the above mentioned warning in almost every ...
Anti's user avatar
  • 153
1 vote
0 answers

Steps for trimming aligned peptides using Trimal

I am trimming the aligned peptide sequences and back translating them to codon using Trimal. Here i am using following cmd's: ...
Kishor Kumar Sarker's user avatar
0 votes
1 answer

list comprehension and codon translation

I'm trying to create a python program that follows the codon translation and turn mRNA sequence into amino acids (see the dictionary). The system has to return an error of the string is not a ...
xin hwa's user avatar
3 votes
2 answers

How to convert Sars-CoV-2 ORF1ab codon positions to ORF1b positions?

Some websites mention amino acid mutations as ORF1ab, most however use ORF1a/b instead. So how can I translate from one to the other? What do I need to subtract from say ...
Cornelius Roemer's user avatar
2 votes
1 answer

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?
NatWH's user avatar
  • 347
1 vote
2 answers

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 ...
Jonathan Charlton's user avatar
1 vote
1 answer

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 ...
Samuel Zimmerman's user avatar
1 vote
1 answer

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 ...
Iakov Davydov's user avatar
3 votes
1 answer

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 ...
PollardMD's user avatar
4 votes
1 answer

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 ...
Furqan's user avatar
  • 87
2 votes
1 answer

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 ...
Mert Metin's user avatar
10 votes
3 answers

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 ...
Iakov Davydov's user avatar
7 votes
1 answer

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 ...
Iakov Davydov's user avatar