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Toolkit: BioInform s Surfing Report: Web-Based Tools from Genome Informatics 2004


Chinook, from the Michael Smith Genome Sciences Center, is an open-source peer-to-peer system for more than 20 bioinformatics algorithms:

CisRED, from the Michael Smith Genome Sciences Center, is a database of conserved motifs determined through orthologous sequences and sequences derived from co-expressed genes:

The CORG (Comparative Regulatory Genomics) database, from the Max-Planck Institute for Molecular Genetics, contains conserved non-coding blocks from human, mouse, rat, fugu, and zebrafish:

DBTSS (Database of Transcriptional Start Sites), from the University of Tokyo, contains accurate transcription start sites of genes, including 13,947 loci for human and 10,591 loci for mouse:

ExonPrimer, from the Institute of Human Genetics at the Technical University of Munich, designs intronic primers for the PCR amplification of exons for resequencing DNA:

Genomemine, from Oxford and Brown Universities, contains sequence and other biological data for 150 bacteria, 547 plasmids, 1,033 viruses, 196 phages, 35 viroids, and 518 organelles:

The Mouse Atlas of Gene Expression, from the British Columbia Cancer Research Center, contains SAGE data for 150 tissues in mouse:

PLAD (Positional Candidate Analysis Display), from the Jackson Laboratory, integrates known and predicted genes on the mouse genome with SNP and functional annotation:

PubFetch, from the Medical College of Wisconsin and collaborators, provides a single interface for multiple literature databases:

PupaSNP Finder, from Spain’s Centro Nacional de Investigaciones Oncologicas, takes as input lists of genes and retrieves SNPs with a potential phenotypic effect:

RESD (Regulatory Element SNPs Database), from Seoul National University, categorizes regulatory elements in human genes and provides a set of SNPs within each area:

SiDE (SiRNA Design), from Spain’s Centro Nacional de Investigaciones Oncologicas, can design a large number of siRNAs with appropriate thermodynamic properties and high specificity:

SiDirect, from the University of Tokyo, is a web-based system for designing target-specific siRNAs:

T1DBase, from the Institute for Systems Biology and collaborators, integrates publicly available genomic data for researchers studying type 1 diabetes:


Filed under

The Scan

Quality Improvement Study Compares Molecular Tumor Boards, Central Consensus Recommendations

With 50 simulated cancer cases, researchers in JAMA Network Open compared molecular tumor board recommendations with central consensus plans at a dozen centers in Japan.

Lupus Heterogeneity Highlighted With Single-Cell Transcriptomes

Using single-cell RNA sequencing, researchers in Nature Communications tracked down immune and non-immune cell differences between discoid lupus erythematosus and systemic lupus erythematosus.

Rare Disease Clues Gleaned From Mobile Element Insertions in Exome Sequences

With an approach called MELT, researchers in the European Journal of Human Genetics uncovered mobile element insertions in exomes from 3,232 individuals with or without developmental or neurological abnormalities.

Team Tracks Down Potential Blood Plasma Markers Linked to Heart Failure in Atrial Fibrillation Patients

Researchers in BMC Genomics found 10 differentially expressed proteins or metabolites that marked atrial fibrillation with heart failure cases.