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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:


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The Scan

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Not Always Trusted

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Identified Decades Later

A genetic genealogy approach has identified "Christy Crystal Creek," the New York Times reports.

Science Papers Report on Splicing Enhancer, Point of Care Test for Sexual Transmitted Disease

In Science this week: a novel RNA structural element that acts as a splicing enhancer, and more.