WTSI Software:

The informatics department has developed many widely used standalone software packages that are available to the research community. These include tools for gene prediction, motif identification and genome search and assembly:

• Analysis
• Sequencing
• Mapping

Ensembl Genome Browser:

Ensembl produces and maintains automatic annotation on selected eukaryotic genomes

VEGA Genome Browser:

Central database repository for high quality manual annotation of vertebrate finished genome sequence

GeneDB:

Annotation from a growing number of organisms is available from the GeneDB web database

Wormbase:

The primary database on the biology and genome of the model organism Caenorhabditis elegans

Ensembl Trace Server:

Public archive of over a billion primary sequence trace files

Human Epigenome Project (HEP):

Provides an epigenetic resource of genome-wide DNA methylation reference profiles in human tissues and cell lines.

Saccharomyces Resequencing Project:

Sequencing and analysis of multiple strains of S cerevisiae and S paradoxus to advance understanding of genomic variation and evolution

Distributed Annotation System:

The Distributed Annotation System (DAS) is a frequently used protocol to openly exchange biological data between decentralized sites over the Internet

Pfam:

Provides a classification of proteins into families and domains using hidden Markov models

iPfam:

Describes Pfam domain interactions that are observed in PDB entries

miRBase:

Provides information about miRNA sequences and predicted target sites

Rfam:

Provides a classification of RNA families using covariance models

MEROPS:

Provides the internationally recognised classification of peptidases and their inhibitors

TreeFam:

Provides curated phylogenetic trees of animal genes, that give reliable ortholog and paralog assignments

Tiffin:

A database of predicted regulatory motifs, a subset with predicted functional annotation

COSMIC:

Database of somatic mutation information in human cancers

DECIPHER:

DatabasE of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources

MitoCheck:

Regulation of mitosis by phosphorylation - a combined functional genomics, proteomics and chemical biology approach

ZF-Models:

Use of zebrafish to make models for human disease and development