Abstract
BackgroundProtein-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.ResultsHere 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. ConclusionsHPIDB 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.
Highlights
Protein-protein interactions (PPIs) play a crucial role in initiating infection in a host-pathogen system
Experimentally identified PPIs are used to search for homologous PPIs to transfer annotations to a new species [15], but the provided tool is limited to predicting intra-species interactions, and has not been applied to predict Host-pathogen protein–protein interactions (HPIs)
Using the web interface The web interface is divided into three separate modules: 1. “Simple search” is used to search the database based on user defined identifiers like UniProt id, Table 1 Summary of representative host and pathogen species in HPIDB
Summary
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. BLASTP cannot be performed in batch mode (multiple sequences at a time), making it difficult to apply for modeling high throughput datasets Another database “Phi-base” catalogues information about experimentally verified pathogenicity, virulence and effector genes from fungal, oomycete and bacterial pathogens, but does not provide any PPI information [9]. Both of these computational studies use intraspecies PPIs to predict inter-species interactions They do not provide any web based tool for predicting HPI. Experimentally identified PPIs are used to search for homologous PPIs to transfer annotations to a new species [15], but the provided tool is limited to predicting intra-species interactions, and has not been applied to predict HPIs
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