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This article is part of the supplement: Proceedings of the 11th Annual Bioinformatics Open Source Conference (BOSC) 2010

Open Access Proceedings

IPRStats: visualization of the functional potential of an InterProScan run

Ryan J Kelly1, David E Vincent1 and Iddo Friedberg12*

Author affiliations

1 Department of Computer Science and Software Engineering, Miami University, Oxford OH 45056, USA

2 Department of Microbiology Pearson Hall, 700 E. High St. Miami University, Oxford OH 45056, USA

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Citation and License

BMC Bioinformatics 2010, 11(Suppl 12):S13  doi:10.1186/1471-2105-11-S12-S13

Published: 21 December 2010

Abstract

Background

InterPro is a collection of protein signatures for the classification and automated annotation of proteins. Interproscan is a software tool that scans protein sequences against Interpro member databases using a variety of profile-based, hidden markov model and positional specific score matrix methods. It not only combines a set of analysis tools, but also performs data look-up from various sources, as well as some redundancy removal. Interproscan is robust and scalable, able to perform on any machine from a netbook to a large cluster. However, when performing whole-genome or metagenome analysis, there is a need for a fast statistical visualization of the results to have good initial grasp on the functional potential of the sequences in the analyzed data set. This is especially important when analyzing and comparing metagenomic or metaproteomic data-sets.

Results

IPRStats is a tool for the visualization of Interproscan results. Interproscan results are parsed from the Interproscan XML or EBIXML file into an SQLite or MySQL database. The results for each signature database scan are read and displayed as pie-charts or bar charts as summary statistics. A table is also provided, where each entry is a signature (e.g. a Pfam entry) accompanied by one or more Gene Ontology terms, if Interproscan was run using the Gene Ontology option.

Conclusions

We present an platform-independent, open source licensed tool that is useful for Interproscan users who wish to view the summary of their results in a rapid and concise fashion.