From kyclark.cshl at gmail.com Fri Dec 3 10:36:40 2010 From: kyclark.cshl at gmail.com (Ken Youens-Clark) Date: Fri, 3 Dec 2010 08:36:40 -0700 Subject: [Gramene-announce] Gramene build 32 released Message-ID: <0AD89987-4514-476F-B554-B3F25A048520@gmail.com> The Gramene team is happy to announce the release of our 32nd build. This release includes the first inclusion of the moss Physcomitrella patens in our Ensembl genome browser which itself is running on the latest version 60. Also new are the chromosome 3 short arms of Oryza nivara and O. rufipogon. Eleven other genomes have been updated, including new genes in O. sativa indica, an update of Arabidopsis thaliana to TAIR version 10, as well as updated Compara complete with new gene trees, whole genome alignments, and a new pairwise dicot synteny build. The genome browsers also have new variation data for A. thaliana and O. sativa japonica and indica. Ensembl functional genomics databases have been updated for four species with new microarray data sets, and our BioMart now includes a variation data set. Our comparative maps now hosts two additional genomes (sorghum, Brachypodium) and a new genetic map from switchgrass, new syntenic block correspondences among our three genomes, and new pre-computed entry points grouped by species of interest (currently just for wheat and sorghum, but more to follow). The pathways section now has the beta releases of MaizeCyc and BrachyCyc, the germplasm database has been updated to host about 12K accessions from four species, and our diversity databases hold new data sets for A. thaliana, rice, and maize. We also have new software improvements for Tassel (version 3.0), our SNP Query tool, and a new beta release of a REST-ful interface to all our databases. For more information, please refer to our release notes: http://www.gramene.org/db/help?state=current_release_notes -- Ken Youens-Clark kclark at cshl.edu Gramene.org Project Manager Ware Lab/CSHL/USDA-ARS From jaiswalp at science.oregonstate.edu Tue Dec 7 18:11:47 2010 From: jaiswalp at science.oregonstate.edu (Pankaj Jaiswal (OSU)) Date: Tue, 07 Dec 2010 15:11:47 -0800 Subject: [Gramene-announce] Releasing MaizeCyc: A metabolic pathway network of maize gene Message-ID: <4CFEBF33.3030802@science.oregonstate.edu> http://news.gramene.org/?p=660 From Gramene News Blog We are pleased to announce the release of the MaizeCyc (http://www.gramene.org/pathway/) database. Developed by the comparative genomics database Gramene (www.gramene.org) and the maize model organism database MaizeGDB (www.maizegdb.org) in collaboration with the Maize Genome Sequencing Project, MaizeCyc is a catalog of known and/or predicted metabolic and transport pathways from Maize (Zea mays mays). Pathways and genes presented in this catalog are based on the annotations carried out by us on the ?filtered gene set? provided as part of the release 4a.53 of the cv. B73 maize genome. The database was created using the Pathway Tools PathoLogic module developed by Peter D. Karp and coworkers at the Bioinformatics Research Group at SRI International. This is a BETA version of the MaizeCyc. In near future a formal release will include annotations from the B73 RefGen_v2 gene models (as part of Release 5a.59), gene names, synonyms and exciting new pathway discoveries. You are welcome to access the same database served from the following mirror sites. Gramene: http://www.gramene.org/pathway/ MaizeGDB: http://maizecyc.maizegdb.org/ We welcome feedback from the research community to help us build a good quality network. You can reach us by sending a message to MaizeCyc curators To learn how to use MaizeCyc, please follow the tutorial. MaizeCyc does not show up on this tutorial which is a bit outdated. However, follow the same instructions to get to the MaizeCyc on the web. This work is supported by the NSF Plant Genome Research Resource grant award #0703908 (Gramene: A Platform for Comparative Plant Genomics) Sincerely Gramene and MaizeGDB project teams