Software

Sockeye

Sockeye is a Java/Java3D application for assembling, viewing and working with genomic information in a direct, interactive and extensible 3D workspace. Designed primarily for phylogenetic footprinting and regulatory element discovery, it lets a user assemble and quickly extract meaning from complex comparative genomics datasets. Sockeye queries and displays EnsEMBL data. It directly queries a gene's orthologues or coexpressed genes. It integrates an extensible library of command-line bioinformatics applications with the 3D workspace through the Chinook application server. It uses JASPAR and TRANSFAC TFBS resources. It offers a powerful environment for work with sequence alignment methods, sequence conservation profiles and conserved regions. It facilitates comparing results from different algorithms and different algorithm parameter settings. It can import and display results in GFF files. It can zoom easily between a whole genome display and a basepair display. InstallAnywhere and WebStart installers are freely available.

Chinook

Chinook is a peer-to-peer (P2P) bioinformatics service. Chinook turns command-line applications into services that are broadcast over a virtual network. A Java application, Chinook was developed to provide compute resources for genome-wide regulatory motif detection. From this, it has grown into a platform that facilitates the exchange of analysis techniques within a local community and worldwide. Currently, over ten analysis services have been made "Chinook-ready". The algorithms range from sequence alignment to regulatory element prediction. Chinook uses XML to make it extremely easy to add new services.

DUNE: Drift Under Neutral Evolution

DUNE is a Java application that transforms an input DNA sequence from one species into an in-silico mutated sequence for another species using a model for molecular evolution that is "neutral"; i.e. occurs with no regions under selective constraint. The source and output can be any species in the application's internal phylogenetic tree, which currently contains: 1) Fugu, zebrafish, chicken, rat, mouse, chimpanzee and human; and 2) C. elegans and C. briggsae. Neutral evolution is modeled by allowing substitution, deletion and insertion events to occur according to parameters in recent published analyses. The package is part of the component in the cisRED production pipeline that estimates p-values for computationally discovered motifs from input sequence sets that include orthologues to the target gene. DUNE is not yet available for licensing; however, if you are interested in using it, please contact us.

HitPlotter

This Java application lets a user quickly evaluate results from one or multiple motif discovery applications. It reads a simple, compact GMM-format text file that is typically generated from a discovery method output report using a Perl script, and displays discovered "motifs" as horizontal coloured lines. This direct display mode lets a user quickly assess discovery datasets that can include hundreds of 'hits' from a large set of different discovery methods, each of which was run with different parameter settings on tens to hundreds of input sequences. The visualization is supported by tools for showing and hiding sequences and datasets, filtering hits by score, etc. Annotations in GMM format (known TFBS, exons, repeats, etc.) can be displayed to give genomic context to hits. 'Hits' from pattern scans can also be displayed, e.g. from 'known' matrices from JASPAR or TRANSFAC. PERL '2gmm' scripts are easily written. They are currently available for ANN-Spec, BioProspector, CONSENSUS, Gibbs Sampler, MDmodule, MDscan, MEME, PhyloCon, Teiresias, MotifSampler, and RSAT oligo-analysis and WCONSENSUS. Although the HitPlotter is still in a pre-beta stage of development, we are willing to license it. Please contact us if you are interested in using it.

cisRED

The cisRED database is available to be run locally. You will need to have a MySQL database server installed. A script is provided which can be run to populate your database. A PDF is also provided which shows a diagram of the cisRED database schema. Please visit our file server at http://www.cisred.org/files/ . From there you will find a listing of all cisRED database releases. Inside each release folder will be a folder named SQL which will contain all of the files needed to set-up and run the database locally.

The code for the cisRED web site is freely available, and can be downloaded and used to run your own mirror of the cisRED web site. You will first need to set-up a copy of the cisRED database. Releases of the cisRED web site are available for download at http://www.cisred.org/files/Software/PloneRED/. If you have questions about this project, including help setting up your mirror, please email Kevin Teague.