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BioInform s Surfing Report: Web-Based Tools and Databases from RECOMB 2003


The annual Research in Computational Molecular Biology conference offers a great showcase for cutting-edge bioinformatics methods, many of which are publicly available through their developers’ websites. A sampling of some of this year’s online crop, from developers in 13 different countries, follows:


3D Hit, from the University of Warsaw and the BioInfoBank Institute in Poznan, Poland, detects structural similarities between proteins by concatenating partial structural alignments:

Arby, a protein structure prediction server, from the Max Planck Institute for Informatics:

DipNet, gel image processing software based on .NET, from Fachhochschule Gelsenkirchen:

GenRGenS from Université Paris-Sud randomly generates genomic sequences and structures for use in detecting over- and under-represented motifs or other bioinformatics applications:

HAP, a method for reconstructing haplotypes from genotype data, from Columbia University:

HaploBlock, software to identify haplotype blocks and resolve haplotypes from genotype data, from Technion:

HMMEd (Hidden Markov Model Editor), a program that designs HHMs for bioinformatics applications, from the Max Planck Institute for Molecular Genetics:

Logic regression software, an adaptive regression methodology for the analysis of SNP microarray data, from Johns Hopkins University and the Fred Hutchinson Cancer Research Center:

Mandala, software to optimize the choice of seeds for particular alignment problems, from Washington University:

MutantDock from the University of Leeds ranks mutations in terms of interaction energy:

PARE (Predicting Association Rate Enhancement), calculates association rates of protein complexes, from the Weizmann Institute of Science and Pennsylvania State University:

PHYDBAC (Phylogenomic Display of Bacterial Genes), from France’s Centre National de la Recherche Scientifique, constructs and displays phylogenomic profiles of bacterial protein sequences:

Sigfind predicts signal peptides in human protein sequences using a bi-directional recurrent neural network, from the University of Pennsylvania, Free University Berlin, MetaGen Pharmaceuticals, and Synaptic:

STACK, from Sweden’s Chalmers University of Technology, is a toolkit for the structural analysis of beta-helical proteins:

TopNet, from Fraunhofer Gesellschaft and Ludwig Maximilians University, visualizes gene networks and expression data:

YASS (Yet Another Similarity Searcher), from Laboratoire Lorrain de Recherche en Informatique et ses Applications, runs at a speed comparable to Blast, but with improved sensitivity:



ASPD (Artificially Selected Proteins/Peptides Database), from the Institute of Cytology and Genetics in Novosibirsk, Russia, integrates phage display data into a network of molecular resources:

Muscle TRAIT, a database of transcripts expressed in human skeletal muscle, from University of Padua in Italy:

ProBiSite from Pontificia Universidad Católica de Chile integrates ligands and protein binding sites from the PDB with the CATH database of structural domains:

ProSplicer, a database of putative alternative splicing information derived from proteins, mRNAs, and ESTs, from National Central University, Taiwan:

SMoS (Structural Motifs of Superfamilies), from India’s National Centre for Biological Sciences, provides information on structural motifs for 110 aligned protein domain superfamilies: SMoS/index.htm.

SNPview, a database of more than 18,000 mouse SNPs, compiled by the Genomics Institute of the Novartis Research Foundation:

SYSTERS (SYSTEmatic Re-Searching) classifies sequences from Swiss-Prot and PIR into family, superfamily, and subfamily clusters, from the Max Planck Institute for Molecular Genetics:

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