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

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Chinook, from the Michael Smith Genome Sciences Center, is an open-source peer-to-peer system for more than 20 bioinformatics algorithms: http://www.bcgsc.bc.ca/chinook/.


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: http://www.cisred.org/.


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: http://corg.molgen.mpg.de/.


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: http://dbtss.hgc.jp/.


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: http://ihg.gsf.de/ihg/ExonPrimer.html.


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: http://www.genomics.ceh.ac.uk/GMINE/.


The Mouse Atlas of Gene Expression, from the British Columbia Cancer Research Center, contains SAGE data for 150 tissues in mouse: http://www.mouseatlas.org/.


PLAD (Positional Candidate Analysis Display), from the Jackson Laboratory, integrates known and predicted genes on the mouse genome with SNP and functional annotation: http://proto.informatics.jax.org/prototypes/plad/.


PubFetch, from the Medical College of Wisconsin and collaborators, provides a single interface for multiple literature databases: http://www.gmod.org/pubfetch/.


PupaSNP Finder, from Spain’s Centro Nacional de Investigaciones Oncologicas, takes as input lists of genes and retrieves SNPs with a potential phenotypic effect: http://pupasnp.bioinfo.cnio.es/.


RESD (Regulatory Element SNPs Database), from Seoul National University, categorizes regulatory elements in human genes and provides a set of SNPs within each area: http://combio.kribb.re.kr/ksnp/resd/.


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: http://side.bioinfo.cnio.es/.


SiDirect, from the University of Tokyo, is a web-based system for designing target-specific siRNAs: http://design.rnai.jp/sidirect/index.php.


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

 

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