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

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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:

SOFTWARE

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

Arby, a protein structure prediction server, from the Max Planck Institute for Informatics: www.mpi-sb.mpg.de/~sommer/Arby/.

DipNet, gel image processing software based on .NET, from Fachhochschule Gelsenkirchen: http://bioinformatik.fh-gelsenkirchen.de/dipnetweb/dipnet.htm.

GenRGenS from Université Paris-Sud randomly generates genomic sequences and structures for use in detecting over- and under-represented motifs or other bioinformatics applications: www.lri.fr/~denise/GenRGenS/.

HAP, a method for reconstructing haplotypes from genotype data, from Columbia University: www1.cs.columbia.edu/compbio/hap/.

HaploBlock, software to identify haplotype blocks and resolve haplotypes from genotype data, from Technion: http://bioinfo.cs.technion.ac.il/haploblock/.

HMMEd (Hidden Markov Model Editor), a program that designs HHMs for bioinformatics applications, from the Max Planck Institute for Molecular Genetics: http://algorithmics.molgen.mpg.de/HMMEd.html.

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: http://bear.fhcrc.org/~ingor/logic/.

Mandala, software to optimize the choice of seeds for particular alignment problems, from Washington University: www.cs.wustl.edu/~jbuhler/mandala/.

MutantDock from the University of Leeds ranks mutations in terms of interaction energy: www.bioinformatics.leeds.ac.uk/group/online/mutdock/index.html.

PARE (Predicting Association Rate Enhancement), calculates association rates of protein complexes, from the Weizmann Institute of Science and Pennsylvania State University: www.weizmann.ac.il/~bcges/PARE.html.

PHYDBAC (Phylogenomic Display of Bacterial Genes), from France’s Centre National de la Recherche Scientifique, constructs and displays phylogenomic profiles of bacterial protein sequences: http://igs-server.cnrs-mrs.fr/phydbac/.

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: http://stepc.stepc.gr/~synaptic/sigfind.html.

STACK, from Sweden’s Chalmers University of Technology, is a toolkit for the structural analysis of beta-helical proteins: www.mdstud.chalmers.se/~md1lars/.

TopNet, from Fraunhofer Gesellschaft and Ludwig Maximilians University, visualizes gene networks and expression data: http://cartan.gmd.de/ToPNet/.

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: www.loria.fr/~noe/.

 

DATABASES

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: http://util.bionet.nsc.ru/databases/aspd/.

Muscle TRAIT, a database of transcripts expressed in human skeletal muscle, from University of Padua in Italy: http://muscle.cribi.unipd.it/.

ProBiSite from Pontificia Universidad Católica de Chile integrates ligands and protein binding sites from the PDB with the CATH database of structural domains: http://protein.bio.puc.cl/cardex/databases/pdb/index.html.

ProSplicer, a database of putative alternative splicing information derived from proteins, mRNAs, and ESTs, from National Central University, Taiwan: http://bioinfo.csie.ncu.edu.tw/ProSplicer/.

SMoS (Structural Motifs of Superfamilies), from India’s National Centre for Biological Sciences, provides information on structural motifs for 110 aligned protein domain superfamilies: http://www.ncbs.res.in/%7Efaculty/mini/ SMoS/index.htm.

SNPview, a database of more than 18,000 mouse SNPs, compiled by the Genomics Institute of the Novartis Research Foundation: http://www.gnf.org/SNP/.

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: http://systers.molgen.mpg.de/.

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