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BioInform s Surfing Report: Software and Databases Discussed at ISMB 2004


BioSigNet-RR, from Arizona State University, is an inference-based approach to representing signaling networks:

CIS (Compound Importance Sampling), from the Hebrew University of Jerusalem, scans regulatory regions for putative binding sites to construct a genome-wide regulatory network:

DECON, from Carnegie Mellon University, combines budding index and gene expression data to deconvolve expression profiles:

DSS (Data Sources Selection), from the Laboratory of Informatics Research at CNRS, is an algorithm that takes a user’s query and preferences into account to provide a list of sources to address a biological query:

HaploBlock, from Technion University, uses high-density haplotype or genotype data top perform linkage disequilibrium:

HyBrow (Hypothesis Browser), from the Huck Institute for Life Sciences at Penn State University, uses a hypothesis ontology to design and evaluate hypotheses:

IMGT/JunctionAnalysis, from the Institute of Human Genetics at CNRS, analyzes immunoglobulin and T-cell receptor junctions:

*MUSCLE, from Robert Edgar, is a multiple sequence alignment program that can align 5,000 sequences of 350 bases in seven minutes on a desktop PC:

Netmotsa, from the Institute for Systems Biology, uses a probabilistic model to predict protein-protein interactions based on protein sequence information and observed physical interactions:

NLProt, from Columbia University, extracts protein names from the scientific literature:

*PROBCONS, from Stanford, is a multiple sequence alignment program:

PSILC (Pseudogene Inference from Loss of Constraint), from the Wellcome Trust Sanger Institute, distinguishes pseudogenes from functional genes:

SCOPEC, from Inpharmatica, is a database of catalytic domains:

TIDE (Terra Incognita Discovery Endeavor), from the Weizmann Institute, assigns gene identities for human ESTs:

Traitmap, from RIKEN, is a database of genetic mapping charts for human, mouse, and Arabidopsis:


*Co-winners of best paper for ISMB 2004.

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