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BioInform s Surfing Report: Web-based Tools and Data from RECOMB 2004


Last week, 650 computational scientists gathered in San Diego for the eighth annual Conference on Research in Computational Molecular Biology — an attendance record, according to organizers. The meeting attracts the world’s leading bioinformatics algorithmists, and is a hotbed for emerging methods that may turn out to be tomorrow’s bioinformatics workhorses. A sampling of some web-based tools discussed at the conference follows.


BOMP (Beta-Barrel Outer Membrane Protein Predictor), from the University of Bergen, predicts whether a sequence from a Gram-negative bacterium is a beta-barrel outer membrane protein:

Genome Fingerprint Scanning, a gene-finding method that uses peptide mass fingerprint data to identify genes in partially sequenced genomes, from the University of North Carolina at Chapel Hill:

CAMP (Comparative Analysis of Metabolic Pathways) calculates the similarities and differences between multiple metabolic pathways in KEGG, from National Yang-Ming University in Taiwan:

Clann, from the National University of Ireland in Maynooth, identifies horizontal gene transfer events via supertree analysis:

e2g, a tool for aligning genomic sequence with cDNA and EST databases, from Bielefeld University:

NCBI has developed a system for identifying gene or protein names that are closely related to a query gene name:

GOArray, from Yale University, identifies genes associated with a term in the Gene Ontology database:

PhlyoBlocks, from Argonne National Laboratory, analyzes protein function using phylogenetic information:

SVMmer, from Argonne National Laboratory, classifies protein families using a support vector machine algorithm:

GOAT (Genome Organization Analysis Tool) compares one or more query genomes against a reference genome to produce a two-dimensional dot plot of matches relative to the reference genome, from Virginia Tech:

TsukubaBB, from AIST in Japan, is a simple heuristic algorithm for motif extraction:

Prober extracts degenerate probes among a set of multiple sequences, from the University of Ulsan College of Medicine in Korea:

GLP (Generalized Local Propensity), from the University of Kansas, identifies sequence segments with high and low conformational flexibility:

HMMerHEAD (HMMer Hashing Enabled Acceleration Device), filters out sequences for HMMer’s hmmsearch program to speed running time 15-fold, from Hebrew University:

ELXR (Exon Locator and Extractor for Resequencing) automates primer set selection, from the University of Texas Southwestern Medical Center:

OPAAS (Optimal, Permuted, and Alternative Alignment of protein Structure), from the Institute of Biomedical Sciences in Taiwan, is a protein structure comparison method based on probability-based matching of secondary structure elements:

PairFold, an algorithm for secondary structure prediction of pairs of RNA molecules, from the University of British Columbia:



The Protein Mutant Resource (PMR), from the San Diego Supercomputer Center, characterizes related artificially mutated structures from the PDB by grouping point mutations of the same structure:

EcoTFs (Escherichia coli Transcription Factors and Signals), from Los Alamos National Laboratory, contains data on 50 transcription factors in E. coli:

MPromDb is a database of mammalian promoters with annotation of the first exon and experimentally supported cis-regulatory elements, from Ohio State University:


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