ORF Finder is a library that with a sequence of nucletotides it finds the all the possible ORFs in the sequence. It will look for a sequence that starts with a start codon and ends with a stop codon. It will default to the beggining of the sequence if it cannot find an ORF long enought with the start codons. It will also use the end of the sequence if no stop codons are present in the sequence reading frame.

Provides nice, programmatic access to fasta and fastq files, as well as providing Sequence and Quality helper classes. No need for BioRuby ;)

Commandline tools for proteomics

Useful class or methods used in qu-* projects.

Light wrapper for RFam data in Ruby.

Rewrite of Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~kenji/subst/) in Ruby programming language

Turns scaffolded contigs and annotations into a genome.

Build a genome scaffold using scaffolder and a set of annotated contigs. This tool updates the locations of the contig annotations using the scaffold template as a base.

Useful Helper methods and classes for testing scaffolder.

Binary to use with scaffolder genome scaffolds

A new ESST generator

'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.

Predict silk-like proteins from its amino acid sequence.

Use the snp-search tool to create, import, manipulate and query your SNP database

Systems Biology Library for Ruby

'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.

A comprehensive wrapper w(RNA)pper for various RNA CLI programs.