A library for exome sequencing data management

Utilities for GFF3, the genome annotation format. Useful to explore the gene model features.

Easy fasta filtering, wrapping, calculating common statistics, sorting etc. Based on the fasta_tool script that I think was written by Jason Stajich.

De-novo assemblies generally only provide draft genomes. FinishM is aimed at improving these draft assemblies.

FULL-LENGTHERNEXT is a tool adapted to NGS technologies, able to work in parallel and in a distributed way to minimise computing time. It is able to classify unigenes to full-length, 5’-end, 3’-end and internal, suggesting which unknown genes are coding or not. It will be also shown that FULL-LENGTHERNEXT fixes frame shifts, one of the main mistake found in wrong entries of full-length sequences databases, and it is a fast tool to compare different transcriptome assemblies.

The tool validates the input predicted genes and provides useful information (length validation, gene merge validation, sequence duplication checking, ORF finding) based on the similarities to genes in public databases.

A Web App wrapper for GeneValidator, a program for validating gene predictions.

This is a development release. Some features are functional at this time. Genfrag allows for rapid in-silico searching of fragments cut by different restriction enzymes in large nucleotide acid databases, followed by matching specificity adapters which allow a further data reduction when looking for differential expression of genes and markers.

Modified version of the bio-svgenes gem, for use in https://geni-act.org education website.

A Sinatra RESTful web-service for sharing RDFized genomic data.

GoRuby makes it easy to interact with the Gene Ontology by using the infrastructure setup in R. By connecting to R using RSRuby, the database and methods can be interrogated. Plus, keeping the R library up to date is much simpler than having to keep a GO implementation up to date.

Library code for Iroki, a phylogenetic tree customization program.

ensembl-api provides a ruby API to the Ensembl databases (http://www.ensembl.org)

Ruby bindings for libssw

Simultaneously perform custom microhomoly strategies for genetic engineering and bioinformatics.

The tools for our laboratory

basic, shared functionality for mspire libraries.

Identify Neuropeptides using powerful Hidden Markov Models. For further information please refer to: https://github.com/wurmlab/neurohmmer

A Web App wrapper for NeuroHmmer, a program for validating gene predictions.

Search for Neuropeptides based solely on the common neuropeptide markers (e.g. signal peptide, dibasic cleavage sites etc.) i.e. not based on homology to known neuropeptides. For more information: https://github.com/wurmlab/npsearch