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New Products: Nov 29, 2011


Researchers from the University of California, Berkeley, and the University of Maryland have released version 1.2.0 of the transcript assembly software Cufflinks here. The new release fixes several bugs and includes accuracy and performance improvements.

The National Center for Biotechnology Information has released its Variation Reporter Tool to match variant calls with variants in dbSNP or dbVar. The new tool is available here, and will provide detailed information on known alleles for the variant call. If the variant is not present in either database it will calculate whether it has a predicted functional consequence.

The NCBI has also added human variant call format files and human genotype XML files by gene to dbSNP, available here via FTP.

Researchers from Johns Hopkins School of Public Health have released Bowtie version 2.0 for aligning sequence reads to the reference. The new release, available here, includes accuracy improvements, speed improvements, and fixes several bugs.

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.