Contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser.
Allows analysis and manipulation of sequence data. SMS can display the genetic code, restriction enzyme set and codon usage table it uses that allowing users to make changes before performing an operation. It provides about 30 utilities easily accessible thank to the web platform. This tool displays results in a unique window directly on the platform. When new analysis are made, new results are added to the precedent.
Detects favored codons for multiple organisms through RNAseq data. corseq is an application that can be used with requiring genomic or annotation information, with the aim of simplifying existing methods. This program is able to determine position and orientation in frame exons within RNAseq reads as well as to consider the most abundant transcripts to calculate codons liable to be more often detected in them.