HPIDB - a unified resource for host-pathogen interactions

BMC Bioinformatics. 2010;11(Suppl 6):S16 DOI 10.1186/1471-2105-11-S6-S16

 

Journal Homepage

Journal Title: BMC Bioinformatics

ISSN: 1471-2105 (Online)

Publisher: BMC

LCC Subject Category: Medicine: Medicine (General): Computer applications to medicine. Medical informatics | Science: Biology (General)

Country of publisher: United Kingdom

Language of fulltext: English

Full-text formats available: PDF, HTML

 

AUTHORS

Kumar Ranjit
Nanduri Bindu

EDITORIAL INFORMATION

Blind peer review

Editorial Board

Instructions for authors

Time From Submission to Publication: 19 weeks

 

Abstract Full Text

<p>Abstract</p> <p>Background</p> <p>Protein-protein interactions (PPIs) play a crucial role in initiating infection in a host-pathogen system. Identification of these PPIs is important for understanding the underlying biological mechanism of infection and identifying putative drug targets. Database resources for studying host-pathogen systems are scarce and are either host specific or dedicated to specific pathogens.</p> <p>Results</p> <p>Here we describe "HPIDB” a host-pathogen PPI database, which will serve as a unified resource for host-pathogen interactions. Specifically, HPIDB integrates experimental PPIs from several public databases into a single, non-redundant web accessible resource. The database can be searched with a variety of options such as sequence identifiers, symbol, taxonomy, publication, author, or interaction type. The output is provided in a tab delimited text file format that is compatible with Cytoscape, an open source resource for PPI visualization. HPIDB allows the user to search protein sequences using BLASTP to retrieve homologous host/pathogen sequences. For high-throughput analysis, the user can search multiple protein sequences at a time using BLASTP and obtain results in tabular and sequence alignment formats. The taxonomic categorization of proteins (bacterial, viral, fungi, etc.) involved in PPI enables the user to perform category specific BLASTP searches. In addition, a new tool is introduced, which allows searching for homologous host-pathogen interactions in the HPIDB database. </p> <p>Conclusions</p> <p>HPIDB is a unified, comprehensive resource for host-pathogen PPIs. The user interface provides new features and tools helpful for studying host-pathogen interactions. HPIDB can be accessed at <url>http://agbase.msstate.edu/hpi/main.html</url>.</p>