Search Results for "codon"

cufCDS calculates codon usage frequency (CUF) of coding sequences (CDSs). The input of this application is a fasta file of coding sequences. The application removes CDSs that are not divisible by 3 and counts the codons of each CDS after removing the start and stop codons. The result for each CDS is reported in the .gcf file. The following files are also produced: .fss, which reports the frequencies of codons used as start and stop signals .lss, which contains the list of start and stop codons of each gene. .cuf, which reports the total frequencies and the fraction of synonymous codons.

With CodonU, you can now easily read, manipulate, and analyze various file formats used in this kind of analysis, and generate high-quality graphics suitable for publishing. This open-source project incorporates various statistical measures necessary for codon usage analysis, including codon adaptation index, codon bias index, Gravy score, and correspondence analysis for both nucleotide and protein sequences. Start using CodonU today and see how it can revolutionize your genomics research! Find more at: https://github.com/SouradiptoC/CodonU Documentation link: https://souradiptoc.github.io/CodonU Example Link: https://github.com/SouradiptoC/CodonU/tree/master/Examples

A simple command-line utility to calculate biological sequence (DNA or protein) sizes in a (multi) FASTA file. It gives averages, GC (or methionine) content, N50, N90, N95, number of N's, and total bases, and can also report by codon if requested.

REDO is a comprehensive application tool for identifying RNA editing events in organelles based on variant call results (VCF files). It is a suite of Perl scripts and can work easily and directly in any operating system installed Perl and R Environment. The stringent rule depended filters and statistical filters are used in REDO for reducing false positive rate. It can provide detailed annotations, statistics and figures for RNA editing sites. REDO also can detect RNA editing events in...

Riboshape is a suite of algorithms to predict ribosome footprint profile shapes from transcript sequences. It applies kernel smoothing to codon sequences to build predictive features, and uses these features to builds a sparse regression model to predict the ribosome footprint profile shapes. Reference: Liu, T.-Y. and Song, Y.S. Prediction of ribosome footprint profile shapes from transcript sequences. Proceedings of ISMB 2016, Bioinformatics, Vol. 32 No. 12 (2016) i183-i191.

codonPhyML uses Markovian codon models of evolution in phylogeny reconstruction. Given a set of species characterized by their DNA sequences as input, codonPhyML will return the phylogenetic tree that best describes their evolutionary relationship. Our paper describing codonPhyML has been published in the journal "Molecular Biology and Evolution" (MBE). For more details, follow the link: http://mbe.oxfordjournals.org/content/30/6/1270. codonPhyML is on the cover of MBE!

VIGOR is a tool for annotating coding genes in viral genomes. It was developed by Jeffrey Hoover and Shiliang Wang for The JCVI Genomic Sequencing Center for Infectious Diseases (GSCID). http://www.biomedcentral.com/content/pdf/1471-2105-11-451.pdf contact: Jeff Hoover 301-540-7858 jefhv@aol.com

CUO is a GUI-based multiplatform software written in Java. It is open source and built with a user/developer-friendly structure. The main function of the software at the current development stage is to optimize genes to be transformed into the Chlamydomonas reinhardtii chloroplast genome although it can be used to optimize genes into other hosts as well. The main tool in CUO, Moptimizer, introduces a semi-automatic way of gene optimization which provides more flexibility and accuracy during...

EvoRadical was written in C. It implements a new codon-based likelihood models for detecting site-specific selection pressures acting on specific physicochemical properties.

CodonW is a programme designed to simplify the Multivariate analysis (correspondence analysis) of codon and amino acid usage. It was written in ANSI compliant C. See the README file for more information.