InterProScan 5: genome-scale protein function classification

Motivation: 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 InterPr...

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Published inBioinformatics Vol. 30; no. 9; pp. 1236 - 1240
Main Authors Jones, Philip, Binns, David, Chang, Hsin-Yu, Fraser, Matthew, Li, Weizhong, McAnulla, Craig, McWilliam, Hamish, Maslen, John, Mitchell, Alex, Nuka, Gift, Pesseat, Sebastien, Quinn, Antony F., Sangrador-Vegas, Amaia, Scheremetjew, Maxim, Yong, Siew-Yit, Lopez, Rodrigo, Hunter, Sarah
Format Journal Article
LanguageEnglish
Published England Oxford University Press 01.05.2014
Subjects
Arabidopsis - chemistry
Arabidopsis - genetics
Bioinformatics
Classification
Cluster Analysis
Computer programs
Data processing
Genome
Genomics - methods
High-Throughput Nucleotide Sequencing - methods
Java (programming language)
Original Papers
Programming Languages
Proteins
Proteins - analysis
Proteins - genetics
Proteins - metabolism
Software
Software packages
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Summary:Motivation: 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. InterProScan is freely available for download from the EMBl-EBI FTP site and the open source code is hosted at Google Code. Availability and implementation: InterProScan is distributed via FTP at ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/ and the source code is available from http://code.google.com/p/interproscan/. Contact: http://www.ebi.ac.uk/support or interhelp@ebi.ac.uk or mitchell@ebi.ac.uk
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Associate Editor: Alfonso Valencia
ISSN:1367-4803
1367-4811
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btu031