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Affymetrix, University of California Santa Cruz, Affymetrix, Perlegen Sciences, Ardais, Allometra, Ensembl 17, MultiFun

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Affymetrix said last week that it has released genotype data for 120,000 validated SNPs through its website (www.affymetrix.com). The data will also be available through the University of California Santa Cruz Genome Browser (www.genome.ucsc.edu) on Oct. 17. The data is from both public SNP databases and the proprietary SNP database developed by Affymetrix subsidiary Perlegen Sciences and is the “first significant SNP database freely available to the public that includes genotype data and allele frequencies for SNPs distributed across the entire human genome,” according to the company. The set was selected from approximately 535,000 SNPs from 54 people, which were tested using the arrays over 8 weeks, to generate about 29 million genotypes. The company then chose the SNPs with "the best distribution across the genome and the highest accuracy and call rates," it said. “Over time, we will put all of the SNPs from the Perlegen database into the public domain,” said Stephen Fodor, chairman and CEO of Affymetrix.


Ardais has released its BIGR (Biomaterials and Information for Genomic Research) Biospecimen Management System, a set of software, protocols, and services to enable researchers to collect, annotate, manage, and distribute human biological material resources. Ardais said it has used the system internally to enroll over 14,000 donors and collect over 180,000 tissue samples for clinical genomics research.


Allometra of Davis, Calif., has released PyMood, a desktop application for visualizing genomic data, for the Mac OS X platform. The software can analyze and display relations between complete genomes, genomic fragments, proteins, ESTs, full-length cDNAs, and expression data, according to the company.


Ensembl 17 is available at http://www.ensembl.org. The release includes a re-annotation of the Anopheles gambiae genome, and the import of dbSNP 116 SNPs for human and mouse.


MultiFun, a classification system for the cellular and physiological roles of Eschericia coli gene products using Gene Ontology terms, is available from the GO Consortium at ftp://ftp.geneontology.org/pub/go/external2go/MultiFun2go.

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