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



ADDA, an algorithm for partitioning protein sequences into domains, from EMBL's structural genomics group:

Clustal-G, from Singapore's Bioinformatics Institute, is a parallel implementation of ClustalW for computational grids:

CONSURF, from Tel Aviv University, identifies functional regions in proteins of known 3D structure:

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

GenDB provides software infrastructure for genome annotation projects, from Bielefeld University:

GoSurfer, from Harvard University, visualizes Gene Ontology information as a tree:

InterViewer, a program for visualizing large-scale protein interaction networks, from Korea's Inha University:

IPPRED, a web-based server from the Bordeaux Center of Bioinformatics, infers protein interactions via homology:

KerDenSOM, a variant of a self-organizing map for microarray data analysis from Spain's National Center for Biotechnology:

MGAlign, from the National University of Singapore, aligns mRNA sequences to genomic sequences:

Rice GAAS, an annotation program to predict rice gene functions, from Japan's National Institute of Agrobiological Sciences:

SAM_T02, a protein structure prediction server from the University of California, Santa Cruz:

Target Explorer, from Columbia University, identifies new target genes for clusters of transcription factor binding sites:

XML Central, from the DNA Data Bank of Japan, offers a set of web services for sequence retrieval from the DBBJ:


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

DrugBank combines drug information with drug target information, from the University of Alberta:

eProteome, a database of motif hits in proteins from 72 genomes, from Stanford University:

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

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:

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

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

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

RED (Rancourt EST Database), from the University of Calgary, a web-based system for the management and dissemination of ESTs:

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

RTKdb, a database of receptor tyrosine kinase sequences, from the Pôle Bio-Informatique Lyonnais:

SOURCE (Stanford Online Universal Resource for Clones and ESTs), from Stanford University, compiles information from several publicly available databases:

Filed under

The Scan

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.