InterProScan 5: genome-scale protein function classification.

Robust large-scale sequence analysis is a major challenge in modern genomic science, where biologists are frequently trying to characterize many millions of sequences. Here, we describe a new Java-based architecture for the widely used protein function prediction software package InterProScan. Developments include improvements and additions to the outputs of the software and the complete reimplementation of the software framework, resulting in a flexible and stable system that is able to use both multiprocessor machines and/or conventional clusters to achieve scalable distributed data analysis.

MyDas, an extensible Java DAS server.

A large number of diverse, complex, and distributed data resources are currently available in the Bioinformatics domain. The pace of discovery and the diversity of information means that centralised reference databases like UniProt and Ensembl cannot integrate all potentially relevant information sources. From a user perspective however, centralised access to all relevant information concerning a specific query is essential.

InterPro in 2011: new developments in the family and domain prediction database.

InterPro (http://www.ebi.ac.

InterPro: the integrative protein signature database.

The InterPro database (http://www.ebi.ac.

Dasty2, an Ajax protein DAS client.

Summary: Dasty2 is a highly interactive web client integrating protein sequence annotations from currently more than 40 sources, using the distributed annotation system (DAS).

Availability: Dasty2 is an open source tool freely available under the terms of the Apache License 2.0, publicly available at http://www.

PRIDE: new developments and new datasets.

The PRIDE (http://www.ebi.ac.

Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.

Background: Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats, making access to this very difficult. The publication and wide implementation of the Human Proteome Organisation Proteomics Standards Initiative Molecular Interactions (HUPO PSI-MI) format in 2004 was a major step towards the establishment of a single, unified format by which molecular interactions should be presented, but focused purely on protein-protein interactions.

PRIDE: a public repository of protein and peptide identifications for the proteomics community.

PRIDE, the 'PRoteomics IDEntifications database' (http://www.ebi.ac.