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BioInform s Surfing Report: Web-Based Tools and Databases from ISMB 2002

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Software

ADDA, an algorithm for partitioning protein sequences into domains, from EMBL's structural genomics group: www.ebi.ac.uk/sgg.

Clustal-G, from Singapore's Bioinformatics Institute, is a parallel implementation of ClustalW for computational grids: www.bii.a-star.edu.sg/~kuobin/clustalg.

CONSURF, from Tel Aviv University, identifies functional regions in proteins of known 3D structure: consurf.tau.ac.il.

Evolutionary Exon Validation, an exon prediction tool from the University of Chicago: nekrut.uchicago.edu/ eev/.

GenDB provides software infrastructure for genome annotation projects, from Bielefeld University: GenDB.Genetik.Uni-Bielefeld.de.

GoSurfer, from Harvard University, visualizes Gene Ontology information as a tree: biosun1.harvard.edu/~szhong/GoSurfer.htm.

InterViewer, a program for visualizing large-scale protein interaction networks, from Korea's Inha University: wilab.inha.ac.kr/protein.

IPPRED, a web-based server from the Bordeaux Center of Bioinformatics, infers protein interactions via homology: cbi.labri.fr/ippred.

KerDenSOM, a variant of a self-organizing map for microarray data analysis from Spain's National Center for Biotechnology: www.engene.cnb.uam.es.

MGAlign, from the National University of Singapore, aligns mRNA sequences to genomic sequences: origin.bic.nus.edu.sg/mgalign/index.html.

Rice GAAS, an annotation program to predict rice gene functions, from Japan's National Institute of Agrobiological Sciences: RiceGaas.dna.affrc.go.jp.

SAM_T02, a protein structure prediction server from the University of California, Santa Cruz: www.soe.ucsc.edu/research/compbio/HMM-apps/T02-query.html.

Target Explorer, from Columbia University, identifies new target genes for clusters of transcription factor binding sites: http://trantor.bioc.columbia.edu/search_for_BS/.

XML Central, from the DNA Data Bank of Japan, offers a set of web services for sequence retrieval from the DBBJ: xml.nig.ac.jp/index.html.

Databases

Atomic Reconstruction of Metabolism, from Keio University, offers atomic-scale components of metabolites to mix and match into possible pathway combinations: www.metabolome.jp.

DrugBank combines drug information with drug target information, from the University of Alberta: www.drugbank.ca.

eProteome, a database of motif hits in proteins from 72 genomes, from Stanford University: fold.Stanford.edu/proteome.

Homophila, from the University of California, San Diego, links human disease genes with their counterparts in Drosophila: homophila.sdsc.edu.

ICBS (Inter-Chain Beta Sheets), a database that identifies, characterizes, and ranks inter-chain beta-sheet interactions within PDB entries, from the University of California, Irvine: www.igb.uci.edu/servers/icbs.

Mooshka, from St. Petersburg State Technical University, is a database for in situ data on gene expression: urchin.spbcas.ru/Mooshka.

PEP (Proteins of Entire Proteomes), from Columbia University, contains protein sequences, their predicted homology to other known sequences, and their predicted secondary structure features: cubic.bioc.Columbia.edu/pep.

The Protein Mutation Resource, from the San Diego Supercomputer Center, lists families of PDB structures related by mutations: pmr.sdsc.edu.

RED (Rancourt EST Database), from the University of Calgary, a web-based system for the management and dissemination of ESTs: 136.159.173.207/ESTs/public/background.php.

RegulonDB, a database on transcriptional regulation and genome organization, from the Universdad Nacional Autónoma de México: www.cifn.unam.mx/ Computational_Genomics/regulondb.

RTKdb, a database of receptor tyrosine kinase sequences, from the Pôle Bio-Informatique Lyonnais: pbil.univ-lyon1.fr/RTKdb.

SOURCE (Stanford Online Universal Resource for Clones and ESTs), from Stanford University, compiles information from several publicly available databases: genome-www5.stanford.edu/cgi-bin/SMD/source/sourceSearch.

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