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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

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NFT of the Web

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In Science this week: genome-wide association study ties variants to white matter stricture in the brain, and more.