bio-gag is a biogem for detecting and correcting a particular type of error that occurs/occurred in particular versions of the IonTorrent DNA sequencing kit. Recent versions of the system don't appear to suffer the same problem

Bioinformatics. Aggregate FastQC (quality control for Next Generation Sequencing -NGS-) results from many different samples in a single web page, with charts and tables organized and simplified. The main goal is to speed up the communication process with colleagues (PIs, Biologists, BioInformatic...

GFF3 (genome browser) information and digest mRNA and CDS sequences. Options for low memory use and caching of records. Support for external FASTA files.

Identify causative mutations in a model genome from NGS reads using the NGM method.

Encode any message string into a DNA sequence

Enables programmatic parsing of HMMER version 3 reports

Parse PFAM HMM definition files so that the models can be accessible programmatically

Hydropathy scale for BioRuby

a programmatic interface to the iPCRess in-silico PCR software. iPCRess is part of the exonerate suite.

A bioruby plugin for calculating the isoelectric point of a protein

Basic tools for parsing, searching, and comparing JASPAR motifs; Based on Bio.motifs module in Biopython

Basic wrapper for the Kallistio Mapper

Provide access to the IlluminaHumanAnnotations. Database comes form Bioconductor's package lumiHumanIDMapping

A biogem for counting small kmers for fingerprinting nucleotide sequences. See README for details.

This is very scrappy at the moment, and will need to be seriously cleaned up. It does what I need it to do for now. I'll fix it up in the coming weeks. Promise :)

Simple, under development Ruby solution for UCSC LiftOver tool

Log4r wrapper for BioRuby

Client package for creating, sending, recieving and consuming SOAP messages from BioModels search engine

Help for working with the output of the .delta files produced by nucmer and promer

Tools to find similarity between pangenomes.