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HIC-Up, Chimp Browser, G-PIPE, ProtoNet v 3.0, GenBank

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An updated version of HIC-Up (Hetero-compound Information Center, Uppsala) is available from the University of Uppsala at http://xray.bmc.uu.se/hicup/release.html. The database now contains information on 4,669 small molecules from the Protein Data Bank, along with several other new features.


The University of California Santa Cruz genome bioinformatics group has released a genome browser and Blat server for the chimpanzee (Pan troglodytes) based on the Nov. 13, 2003, Arachne assembly produced by the Chimpanzee Genome Sequencing Consortium. The Chimp Browser is available at http://genome.cse.ucsc.edu/cgi-bin/hgGateway?org=Chimp.


G-PIPE, a workflow generator for PISE and EMBOSS, is available from Colombia’s Fundación Universitaria San Martín at http://sirio.sanmartin.edu.co/Pise/gpipe.html. The package allows users to define and monitor workflows for bioinformatics experiments.


ProtoNet v 3.0, an automatic classification of more than a million protein sequences from UniProt based on hierarchical clustering, is available from Hebrew University in Jerusalem at http://www.protonet.cs.huji.ac.il/.


GenBank release 140.0 is now available from NCBI at ftp://ftp.ncbi.nih.gov/. The release contains 37,893,844,733 base pairs and 32,549,400 entries, up by 1,340,476,248 base pairs and 1,580,982 sequence records from the December 139.0 release. Uncompressed, the 140.0 flat files require about 127 GB for the sequence files only. The ASN.1 version requires around 113 GB.

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The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

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.