Skip to main content
Premium Trial:

Request an Annual Quote

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

Premium

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.

Filed under

The Scan

Driving Malaria-Carrying Mosquitoes Down

Researchers from the UK and Italy have tested a gene drive for mosquitoes to limit the spread of malaria, NPR reports.

Office Space to Lab Space

The New York Times writes that some empty office spaces are transforming into lab spaces.

Prion Pause to Investigate

Science reports that a moratorium on prion research has been imposed at French public research institutions.

Genome Research Papers on Gut Microbe Antibiotic Response, Single-Cell RNA-Seq Clues to Metabolism, More

In Genome Research this week: gut microbial response to antibiotic treatment, approach to gauge metabolic features from single-cell RNA sequencing, and more.