From maurel at ebi.ac.uk Fri Dec 6 10:19:46 2013 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Fri, 6 Dec 2013 10:19:46 +0000 Subject: [ensembl-announce] Ensembl release 74 is out! Message-ID: <390EF4C2-1F35-466C-A732-8178CDD7D7A3@ebi.ac.uk> We are pleased to announce that the latest Ensembl update (e!74) has been released : http://www.ensembl.org/ Highlights of this release include: Human: Updated patches for the human assembly (GRCh37.p13) Updated human GENCODE release 19 Updated dbSNP 138 data for human New species: Sheep (Ovis aries) Cave fish (Astyanax mexicanus) Spotted gar (Lepisosteus oculatus) Other species: Updated patches for the mouse assembly (GRCm38.p2) Updated mouse GENCODE release M2 Updated assembly for armadillo (Dasnov3.0), including RNASeq data Other news: New page displaying ncRNA secondary structure New matrix configuration for RNASeq models for human, sheep and opossum A complete list of the changes in release 74 can be found at http://www.ensembl.org/info/website/news.html For the latest news from the Ensembl project visit our blog at http://www.ensembl.info The release blog post can be viewed here: http://www.ensembl.info/blog/2013/12/06/ensembl-74-has-been-released/ Best Regards, Thomas -- Thomas Maurel Bioinformatician - Ensembl Production Team European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom -------------- next part -------------- An HTML attachment was scrubbed... URL: From maurel at ebi.ac.uk Fri Dec 13 09:12:16 2013 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Fri, 13 Dec 2013 09:12:16 +0000 Subject: [ensembl-announce] Declarations of intentions for Ensembl Release 75 Message-ID: <69339A28-6AB3-4D0B-827C-027B9A0FE326@ebi.ac.uk> Dear all, Please find the summary of the declarations of intentions for Ensembl release 75 (scheduled for the 18th of February 2014) on our public website: http://admin.ensembl.org/Changelog/Summary Note these are intentions and are not guaranteed to be in the release. Best regards, Thomas Maurel -- Thomas Maurel Bioinformatician - Ensembl Production Team European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom -------------- next part -------------- An HTML attachment was scrubbed... URL: From dstaines at ebi.ac.uk Thu Dec 19 16:57:34 2013 From: dstaines at ebi.ac.uk (Dan Staines) Date: Thu, 19 Dec 2013 16:57:34 +0000 Subject: [ensembl-announce] Ensembl Genomes Release 21 Message-ID: <52B3257E.5040202@ebi.ac.uk> Dear all, We have just released the latest update of Ensembl Genomes. This release contains the chromosome survey sequence for bread wheat cv Chinese Spring, generated by the International Wheat Genome Sequencing Consortium. More than 100,000 protein-coding genes predicted by MIPS in bread wheat are now available for the first time in Ensembl Plants. We also provide in this release functional annotation, genome alignments, and inferred evolutionary histories for bread wheat. The other highlights of release 21 are: New genomes Ensembl Fungi Verticillium dahliae and three new Schizosaccharomyces species (S. cryophilus, S. octosporus and S. japonicus) Ensembl Protists Emiliania huxleyi Ensembl Metazoa Dendroctonus ponderosae and Solenopsis invicta Ensembl Bacteria 675 new genomes added (9,764 genomes now represented in total) New data Ensembl Fungi Pairwise DNA alignments for Schizosaccharomyces and Magnaporthe species, and for Ustilago maydis and Sporisorium reilianum Ensembl Protists Pairwise alignments for Alveolates, Stramenopiles, Amoebozoa and Kinetoplastida Ensembl Plants Gene models for T. aestivum chromosome survey sequences, as described above Additional wheat RNA-Seq data. DNA-DNA alignments between bread wheat, rice, and Brachypodium distachyon. MSU-7 gene models for the rice genome are now available, allowing visual comparison between this and the IRGSP set. Cross-references between the MSU and IRGSP gene sets are provided by rap-db, so searching and querying using either identifier space is possible. Updated data Ensembl Fungi Peptide comparative genomics and BioMart Schizosaccharomyces pombe annotations from PomBase Ensembl Metazoa Peptide comparative genomics and BioMart Ensembl Plants Updated gene-trees to include T. aestivum gene models. Updated GO terms for O. sativa and projected to other species. Updated repeat analysis (TREP) for wheat genomes If you have any questions or comments, drop us a line on helpdesk at ensemblgenomes.org The Ensembl Genomes Team -- Dan Staines, PhD Technical Coordinator, Ensembl Genomes European Bioinformatics Institute (EMBL-EBI) http://www.ebi.ac.uk/ http://www.ensemblgenomes.org/ From maurel at ebi.ac.uk Fri Dec 6 10:19:46 2013 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Fri, 6 Dec 2013 10:19:46 +0000 Subject: [ensembl-announce] Ensembl release 74 is out! Message-ID: <390EF4C2-1F35-466C-A732-8178CDD7D7A3@ebi.ac.uk> We are pleased to announce that the latest Ensembl update (e!74) has been released : http://www.ensembl.org/ Highlights of this release include: Human: Updated patches for the human assembly (GRCh37.p13) Updated human GENCODE release 19 Updated dbSNP 138 data for human New species: Sheep (Ovis aries) Cave fish (Astyanax mexicanus) Spotted gar (Lepisosteus oculatus) Other species: Updated patches for the mouse assembly (GRCm38.p2) Updated mouse GENCODE release M2 Updated assembly for armadillo (Dasnov3.0), including RNASeq data Other news: New page displaying ncRNA secondary structure New matrix configuration for RNASeq models for human, sheep and opossum A complete list of the changes in release 74 can be found at http://www.ensembl.org/info/website/news.html For the latest news from the Ensembl project visit our blog at http://www.ensembl.info The release blog post can be viewed here: http://www.ensembl.info/blog/2013/12/06/ensembl-74-has-been-released/ Best Regards, Thomas -- Thomas Maurel Bioinformatician - Ensembl Production Team European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom -------------- next part -------------- An HTML attachment was scrubbed... URL: From maurel at ebi.ac.uk Fri Dec 13 09:12:16 2013 From: maurel at ebi.ac.uk (Thomas Maurel) Date: Fri, 13 Dec 2013 09:12:16 +0000 Subject: [ensembl-announce] Declarations of intentions for Ensembl Release 75 Message-ID: <69339A28-6AB3-4D0B-827C-027B9A0FE326@ebi.ac.uk> Dear all, Please find the summary of the declarations of intentions for Ensembl release 75 (scheduled for the 18th of February 2014) on our public website: http://admin.ensembl.org/Changelog/Summary Note these are intentions and are not guaranteed to be in the release. Best regards, Thomas Maurel -- Thomas Maurel Bioinformatician - Ensembl Production Team European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom -------------- next part -------------- An HTML attachment was scrubbed... URL: From dstaines at ebi.ac.uk Thu Dec 19 16:57:34 2013 From: dstaines at ebi.ac.uk (Dan Staines) Date: Thu, 19 Dec 2013 16:57:34 +0000 Subject: [ensembl-announce] Ensembl Genomes Release 21 Message-ID: <52B3257E.5040202@ebi.ac.uk> Dear all, We have just released the latest update of Ensembl Genomes. This release contains the chromosome survey sequence for bread wheat cv Chinese Spring, generated by the International Wheat Genome Sequencing Consortium. More than 100,000 protein-coding genes predicted by MIPS in bread wheat are now available for the first time in Ensembl Plants. We also provide in this release functional annotation, genome alignments, and inferred evolutionary histories for bread wheat. The other highlights of release 21 are: New genomes Ensembl Fungi Verticillium dahliae and three new Schizosaccharomyces species (S. cryophilus, S. octosporus and S. japonicus) Ensembl Protists Emiliania huxleyi Ensembl Metazoa Dendroctonus ponderosae and Solenopsis invicta Ensembl Bacteria 675 new genomes added (9,764 genomes now represented in total) New data Ensembl Fungi Pairwise DNA alignments for Schizosaccharomyces and Magnaporthe species, and for Ustilago maydis and Sporisorium reilianum Ensembl Protists Pairwise alignments for Alveolates, Stramenopiles, Amoebozoa and Kinetoplastida Ensembl Plants Gene models for T. aestivum chromosome survey sequences, as described above Additional wheat RNA-Seq data. DNA-DNA alignments between bread wheat, rice, and Brachypodium distachyon. MSU-7 gene models for the rice genome are now available, allowing visual comparison between this and the IRGSP set. Cross-references between the MSU and IRGSP gene sets are provided by rap-db, so searching and querying using either identifier space is possible. Updated data Ensembl Fungi Peptide comparative genomics and BioMart Schizosaccharomyces pombe annotations from PomBase Ensembl Metazoa Peptide comparative genomics and BioMart Ensembl Plants Updated gene-trees to include T. aestivum gene models. Updated GO terms for O. sativa and projected to other species. Updated repeat analysis (TREP) for wheat genomes If you have any questions or comments, drop us a line on helpdesk at ensemblgenomes.org The Ensembl Genomes Team -- Dan Staines, PhD Technical Coordinator, Ensembl Genomes European Bioinformatics Institute (EMBL-EBI) http://www.ebi.ac.uk/ http://www.ensemblgenomes.org/