Skip to main content
Premium Trial:

Request an Annual Quote

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:

Filed under

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.