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Nucleic Acids Research, UCSC genome browser, GenBank, Beacon Designer 4.0, GoKinD, CEPH, mzData, KlusterCaller

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Nucleic Acids Research has published its annual database issue, which includes papers describing 719 molecular biology data resources, 171 more than the 2004 database issue. The issue is freely available to subscribers and non-subscribers at http://nar.oupjournals.org/content/vol33/suppl_1/.


The University of California Santa Cruz Genome Bioinformatics Group has released a genome browser for the Apis mellifera (honeybee) assembly at http://genome.ucsc.edu/cgi-bin/hgGateway?db=apiMel1. The assembly is around 213 Mb.


GenBank release 145.0 is now available via ftp from the National Center for Biotechnology Information at ftp://ftp.ncbi.nih.gov/. The release contains 44,575,745,176 base pairs and 40,604,319 entries. Uncompressed, the 144.0 flat files require about 153 GB for the sequence files only. The ASN.1 version requires around 133 GB.


Premier Biosoft has released Beacon Designer 4.0 for designing primers and probes for single or multiplex qPCR assays. A demo version is available at http://www.premierbiosoft.com/molecular_beacons/index.html.


The National Institutes of Health, Juvenile Diabetes Research Foundation, and Centers for Disease Control and Prevention have launched GoKinD (Genetics of Kidneys in Diabetes), a collection of biosamples and data on the genetic causes of kidney disease in type 1 diabetes. Researchers can apply for DNA, clinical data, and genetic data at http://www.gokind.org/access.


The Foundation Jean Dausset-Centre d’Etude du Polymorphisme Humain (CEPH) has released the latest version of its database of genotypes for genetic markers that have been typed on the CEPH reference family resource for linkage mapping. Version 10.0 of the database contains genotypes for 32,356 genetic markers, and is available at http://www.cephb.fr/cephdb.


Version 1.05 of the mzData mass spec data exchange format is available at http://psidev.sourceforge.net/ms/#mzdata. The update includes enhanced annotation of almost all schema elements, according to the Protein Standards Initiative development team.


KBiosciences has released KlusterCaller, a genotyping software package that uses fluorescent clustering techniques to visualize, auto-call, format, and manage projects. A free trial is at http://www.kbioscience.co.uk/software/klustercaller/.

 

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The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.