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Downloads and Upgrades: Sep 23, 2011

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This week, the Fox Chase Cancer Center announced that it has updated the Protein Common Interface Database, ProtCID, a repository of clusters of common interfaces observed in multiple crystal structures of homologous proteins.

Updates include improvements in how PFAM domains are assigned to structures in the Protein Data Bank; and Pymol script files for the interface superposition of a cluster are now included in the cluster interfaces' tar.gz files


Ingenuity has added new miRNA data to Ingenuity Pathway Analysis.

The company said it has included new experimentally validated miRNA-mRNA target interactions from miRecords, plus thousands of additional miRNA-mRNA interactions manually curated from additional peer-reviewed literature.

Ingenuity said the new content will improve the ability of IPA's miRNA target filter to help researchers prioritize miRNA target interactions.


Reactome 38 is available here.

The release includes new topics on grouping pathways for meiotic recombination; nodal signaling; signal transduction; and metabolism. Furthermore, a new Reactome tutorial has been published.


The GenePattern development team at the Broad Institute has released GenePattern Archive, or GParc.

According to the developers, GParc is a place to share modules and help grow the GenePattern community. Users can make GenePattern modules that they have created available to the bioinformatics community by creating an account and uploading modules to GParc.


The Scan

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.