Tag Archives: protein analysis

Guest Post: iRefWeb — Andrei Turinsky

This next post in our continuing semi-regular Guest Post series is from Andrei Turinsky, one of the developers of iRefWeb. If you are a provider of a free, publicly available genomics tool, database or resource and would like to convey something to users on our guest post feature, please feel free to contact us at wlathe AT openhelix DOT com or the contact form (write ‘guest post’ as subject heading). We welcome introductions to your resource, information on updates, highlights of little known gems or opinion pieces on the state of genomic research and databases.

What is iRefWeb?

Protein-protein interactions (PPI) have become an important tool in biomedical research. Yet the PPI data for a specific organism tend to be distributed over a number of different databases. Comparison and integration of PPI information across databases remains a challenging task.

iRefWeb (Turner et al. (2010) Database, Vol. 2010, Article ID baq023.) is a web interface to a broad integrated landscape of protein-protein interactions (PPIs). For a given gene or protein, you can access all PPI records and protein complexes, consolidated non-redundantly from ten major public databases: BIND, BioGRID, CORUM, DIP, IntAct, HPRD, MINT, MPact, MPPI and OPHID. iRefWeb also presents various supporting evidence, helping you to gauge the reliability of an interaction. Versatile search filters allows you to retrieve the PPIs with a given level of support. Other features facilitate the analysis of possible inconsistencies across PPI data and the examination of PPI statistics. Data consolidation procedure effectively combines redundant records using the iRefIndex process (Razick et al (2008) BMC Bioinformatics 9, 405.).

Figure 1: The iRefIndex process aggregated over 916,059 original PPI records from source databases, 75% of which were redundant. The consolidation merged the redundant PPIs, reducing their number four-fold (orange). Only 232,612 PPIs were non-redundant (blue)

Continue reading

Tip of the Week: Collection of Proteomics Tools at ExPASy, including Radar

I’ve blogged about ExPASy in the past, and today my tip is based at this WONDERFUL site. In the tip I will briefly introduce you to a list of proteomic tools that cover a wide range of functions you may need to apply to your favorite sequence or sequences, and demonstrate one such tool. These tools are both from the ExPASy team and from other providers. Each tool is described and links to it are provided. The tools are organized into categories of functions for easier perusing of the list. I feature a repeat finder named Radar.

If you find one you love (or can’t live without) in this list PLEASE do let us know!  Happy proteomics to you!