Codetta: predicting the genetic code from nucleotide sequence
Yekaterina Shulgina, Sean R. Eddy
Abstract
SUMMARY: Codetta is a Python program for predicting the genetic code table of an organism from nucleotide sequences. Codetta can analyze an arbitrary nucleotide sequence and needs no sequence annotation or taxonomic placement. The most likely amino acid decoding for each of the 64 codons is inferred from alignments of profile hidden Markov models of conserved proteins to the input sequence. AVAILABILITY AND IMPLEMENTATION: Codetta 2.0 is implemented as a Python 3 program for MacOS and Linux and is available from http://eddylab.org/software/codetta/codetta2.tar.gz and at http://github.com/kshulgina/codetta. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Topics & Concepts
Python (programming language)Computer scienceGenetic codeAnnotationSoftwareSequence (biology)Computational biologyProgramming languageSource codeSequence alignmentSequence logoNucleic acid sequenceBiologyGeneticsBioinformaticsPeptide sequenceAmino acidGeneRNA and protein synthesis mechanismsGenomics and Phylogenetic StudiesMachine Learning in Bioinformatics