Software

cisRED

For earlier versions of cisRED, we made the database and web site code available for installation on any system that runs Plone v2.0 and a MySQL database server. We now offer for download only the MySQL CREATE TABLE files and the full table data. With these, you can install a local cisRED that you can query with SQL, as you can query the current version of the database at db.cisred.org. Documentation for the schema, table properties and typical SQL queries is available from the Databases & Methods area. Because we continue to evolve the cisRED schema and data, if you are interested in running cisRED locally, please contact us at cisred@bcgsc.ca for the latest status information.

ORegAnno

The Open REGulatory ANNOtation database (ORegAnno) is an open database for the curation of known regulatory elements from scientific literature. Annotation is collected from users worldwide for various biological assays and is automatically cross-referenced against PubMED, Entrez Gene, EnsEMBL, dbSNP, and the Taxonomy database, where appropriate, with information regarding the original experimentation performed (evidence). ORegAnno further provides an open validation process for all regulatory annotation in the public domain. Assigned validators receive notification of new records in the database and are able to cross-reference the citation to ensure record integrity. Validators have the ability to modify any record (deprecating the old record and creating a new one) if an error is found. Further, any contributor to the database can comment on any annotation by marking errors, or adding special reports into function as they see fit. These features of ORegAnno ensure that the collection is of the highest quality and uniquely provides a dynamic view of our changing understanding of gene regulation in the various genomes.

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, CisModule, 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.