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BMC Bioinformatics. 2010 Oct 7;11 Suppl 6:S16. doi: 10.1186/1471-2105-11-S6-S16.

HPIDB--a unified resource for host-pathogen interactions.

Author information

1
College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA. rkumar@cvm.msstate.edu

Abstract

BACKGROUND:

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.

RESULTS:

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.

CONCLUSIONS:

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 http://agbase.msstate.edu/hpi/main.html.

PMID:
20946599
PMCID:
PMC3026363
DOI:
10.1186/1471-2105-11-S6-S16
[Indexed for MEDLINE]
Free PMC Article

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