From rhoda at ebi.ac.uk Tue Jul 5 08:28:43 2011 From: rhoda at ebi.ac.uk (Rhoda Kinsella) Date: Tue, 5 Jul 2011 08:28:43 +0100 Subject: [ensembl-announce] Ensembl release 63 Message-ID: The Ensembl project is pleased to announce release 63 of Ensembl (http://www.ensembl.org ) which was released on June 30th. Highlights include a new high-coverage assembly for microbat (Myotis lucifugus), the most recent human and zebrafish manual gene annotations from HAVANA and a fresh update of mouse variation data, among numerous other additions. For more information about this release visit: http://www.ensembl.org/info/website/news.html For the latest news on the ensembl project visit our blog at http://www.ensembl.info The release blog post can be viewed here: http://www.ensembl.info/blog/2011/06/30/ensembl-63-is-out Regards Rhoda Kinsella Rhoda Kinsella Ph.D. Ensembl Bioinformatician, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK. From st3 at sanger.ac.uk Wed Jul 6 10:35:35 2011 From: st3 at sanger.ac.uk (Stephen Trevanion) Date: Wed, 06 Jul 2011 10:35:35 +0100 Subject: [ensembl-announce] ensembl archive website downtime Message-ID: <4E142C67.8010000@sanger.ac.uk> Dear all, The ensembl archive websites will be unavailable for a period of a few hours starting from 10am BST on Fri 8th July. This is required for some essential hardware maintenance. We apologise for any inconvenience this might cause. Steve Trevanion From jeff at ebi.ac.uk Tue Jul 12 15:07:15 2011 From: jeff at ebi.ac.uk (Jeff Almeida-King) Date: Tue, 12 Jul 2011 15:07:15 +0100 Subject: [ensembl-announce] Ensembl Genomes release 10 Message-ID: <4E1C5513.6020405@ebi.ac.uk> The Ensembl Genomes Project is pleased to announce release 10 of Ensembl Genomes. The main highlights of this release are: * Software migration to Ensembl 63 * /Trypanosoma brucei/, a causative agent of Human African trypanosomiasis, or sleeping sickness genome added to Ensembl Protists . * /Ustilago maydis/ (Plant-pathogen interaction model)/, //Puccinia triticina /(wheat rust fungus) and /Nectria haematococca / (Plant pathogen) added to Ensembl Fungi. * Latest 1001 Genomes release included for /Arabidopsis thaliana, /together with 5 additional gene models from TAIR10. Projection of GO terms from /Arabidopsis thaliana/ and /Oryza sativa japonica/ to other species based on homology, also added for Ensembl Plants . -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: jeff.vcf Type: text/x-vcard Size: 290 bytes Desc: not available URL: From mr6 at sanger.ac.uk Wed Jul 13 14:35:48 2011 From: mr6 at sanger.ac.uk (Magali Ruffier) Date: Wed, 13 Jul 2011 14:35:48 +0100 Subject: [ensembl-announce] Intentions for Ensembl Release 64 Message-ID: <4E1D9F34.1080101@sanger.ac.uk> An HTML attachment was scrubbed... URL: From mr6 at sanger.ac.uk Fri Jul 15 09:05:21 2011 From: mr6 at sanger.ac.uk (Magali Ruffier) Date: Fri, 15 Jul 2011 09:05:21 +0100 Subject: [ensembl-announce] Intentions for Ensembl Release 64 Message-ID: <4E1FF4C1.4080409@sanger.ac.uk> Hi, Please see below a list of intentions declared for Ensembl release 64 (scheduled for September). Please not that these are intentions and are not guaranteed to be in the release. Thanks, Magali ======================================= Declarations of Intentions - Ensembl 64 ======================================= Compara ======= Pairwise alignments (All Species) --------------------------------- ~ human vs cow lastz alignments ~ human vs tasmanian devil lastz alignments ~ human haplotype alignments for high coverage blastz-net alignments ~ human vs lamprey tblat alignments ~ lamprey vs Ciona intestinalis tblat alignments ~ lamprey vs Danio rerio tblat alignments ~ lamprey vs Gasterosteus aculeatus tblat alignments Multiple alignments (All Species) --------------------------------- ~ 12way-mammal EPO alignments to incorporate new cow ~ 19way-amniota Pecan alignments to incorporate new cow ~ 35way-mammal low-coverage-EPO alignments (new cow) Syntenies (All Species) ----------------------- ~ human-cow synteny ProteinTrees and homologies (All Species) ----------------------------------------- GeneTrees (protein-coding) with new/updated genebuilds and assemblies ~ Clustering using hcluster_sg ~ Multiple sequence alignments using MCoffee without the exon-disaligner module, or Mafft ~ Phylogenetic reconstruction using TreeBeST ~ Homology inference including the recent 'possible_ortholog','putative gene split' and 'contiguous gene split' exceptions ~ Pairwise gene-based dN/dS scores for high coverage species pairs only (both on orthologues and paralogues) ~ GeneTree stable ID mapping ncRNAtrees and homologies (All Species) --------------------------------------- ~ Classification based on Rfam model ~ Multiple sequence alignments with infernal ~ Phylogenetic reconstruction using RaxML ~ Phylogenetic reconstruction using FastTree2 and RaxML-light for very big families ~ Additional multiple sequence alignments with Prank (w/ genomic flanks) ~ Additional phylogenetic reconstruction using PhyML and NJ ~ Phylogenetic tree merging using TreeBeST ~ Homology inference Protein Families (All Species) ------------------------------ Updated MCL families including all Ensembl transcript isoforms and newest Uniprot Metazoa. ~ Clustering by MCL ~ Multiple Sequence Alignments with MAFFT ~ Family stable ID mapping Compara dumps (All Species) --------------------------- ~ EMF dumps for 20 way PECAN multiple aligments ~ BED files for 20 way GERP constrained elements ~ EMF dumps for 12 way EPO multiple aligments ~ EMF dumps for 35 way low-coverage alignments ~ BED files for 35 way low-coverage alignments ~ Data dumps for ProteinTrees ~ Data dumps for ncRNAtrees API/schema changes (All Species) -------------------------------- ~ changes in the class hierarchy (NestedSet-Member-AlignedMember) to achieve better flexibility and fight code redundancy ~ possible changes in the schema: adding a new "header" table for a tree root, moving general properties of the tree into that table ~ possible changes in the schema: adding tables for tree's properties and node's properties to make tag storage and extraction more efficient Core ==== Xref projections (All Species) ------------------------------ Project GO IDs and gene names to species. Xrefs (All Species) ------------------- Update xrefs for human, mouse, sea squirt ciona intestinalis and ciona savignyi, madagascar hedgehog, western european hedgehog, mouse lemur, platypus, bushbaby, shrew, squirrel schema change (All Species) --------------------------- is_ref will be added to the alt_allele table to show which is the reference gene. Embl/ Genbank flat file dumps (All Species) ------------------------------------------- Schema version update (All Species) ----------------------------------- patch_63_64_a.sql update schema version to 64 LRG import (Human) ------------------ Import of new LRG sequences Funcgen ======= New Regulatory Data (Human and Mouse) ------------------------------------- ~ New Mouse MEL cell-line regulatory build, including Dnase-Seq, and ChIP-Seq for p300, cMyb, USF2, Rad21, NELFe and Max. All data is from ENCODE, following their data policies. ~ New Human CD4 ChIP-Seq data for CBP, p300, MOF, PCAF, Tip60, HDAC1, HDAC2, HDAC3 and HDAC6 (Wang et al, 2009). A new regulatory build was made to incorporate this data. MotifFeatures: Scores Rounded (All Species) ------------------------------------------- MotifFeature scores were rounded to 3 decimal places. MicroArray Mapping (Human, Mouse and Rat) ----------------------------------------- Micro array mapping has been performed for those species with new assemblies or updated gene builds. DNA methylation DAS tracks (Human) ---------------------------------- We have updated the set of DNA methylation DAS tracks using data available from the ENCODE project. patch_63_64_a - Schema version (All Species) -------------------------------------------- The schema_cersion entry in the meta table has been patched to version 64. patch_63_64_b - Cell type experimental factor ontology ID (All Species) ----------------------------------------------------------------------- The cell_type table has had an efo_id field added to represent links to the Experimental Factor Ontology. patch_63_64_c - Experimental meta data (All Species) ---------------------------------------------------- A patch has been applied to add fields to capture experimental meta data e.g. archive & pubmed IDs Genebuild ========= Lamprey genome (Lamprey) ------------------------ A full annotated gene set for the lamprey genome Human cDNA update (Human) ------------------------- New cDNA db for human. GRCh37.p5 (Human) ----------------- Adding the fifth patch release for the human assembly. This alters the assembly information in all human databases. GRCh37.p5 annotation (Human) ---------------------------- Annotation of the patches in the other features db, including projection of annotation from the primary assembly. Cow genebuild (Cow) ------------------- A new genebuild has been done on the cow UMD 3.1 assembly. A new otherfeatures database has also been prepared. Mouse gene set update (Mouse) ----------------------------- The merged gene set has been updated to incorporate the latest Vega manual annotation. Tasmanian Devil Genome (Tasmanian devil) ---------------------------------------- A genebuild on the Tasmanian Devil 7.0 assembly has been created along with an otherfeatures database containing RNASeq models. Update to Ensembl-Havana GENCODE gene set (release 9) (Human) ------------------------------------------------------------- Update to Ensembl-Havana GENCODE gene set (release 9) based on Ensembl gene set and latest Havana gene annotation. GENCODE RNA-Seq (Human) ----------------------- ----------------------- Human Vega annotation (Human) ----------------------------- Manual annotation of human from Havana has been updated. This represents the annotation presented in Vega release 44. Annotation by Havana of chromosome 14 has been completed. Mouse Vega annotation (Mouse) ----------------------------- Manual annotation of mouse from Havana has been updated, including annotation of the MHC region on chromosome 17. The data represents the annotation presented in Vega release 44. Mouse cDNA update (Mouse) ------------------------- The latest set of cDNAs for mouse (as of dd/mon/yyyy) from the European Nucleotide Archive and NCBI RefSeq were aligned to the current genome using Exonerate.There are nnnn new cDNA for Ensembl 64. Flagging obsolete Uniprot proteins (All Species) ------------------------------------------------ Flag the obsolete proteins in Uniprot used as supporting evidence Flagging obsolete Ensembl proteins (All Species) ------------------------------------------------ Flag obsolete human Ensembl proteins used as supporting evidence Gorilla 3.1 projection (Gorilla) -------------------------------- A new AGP file has been provided for gorilla, using the same contigs but with different gaps sizes. Genes from the e63 release will be projected onto the updated assembly. Removal of ambiguous bases from Takifugu rubripes (Fugu) -------------------------------------------------------- Removed the 'R' and 'Y' ambiguous bases from scaffold_20 in takifugu_rubripes_core_64_4. Mart ==== Ensembl 64 mart databases (All Species) --------------------------------------- Full build of all seven marts for release 64 Variation ========= dbSNP 133 import (Cow) ---------------------- dbSNP Build 133 for cow based on the UMD_3.1 assembly. LRG variant import (Human) -------------------------- variants on LRG sequences Phenotype annotations (Human) ----------------------------- ~ COSMIC import update. Minor changes in COSMIC sample names ~ OMIM, NHGRI GWAS catalog, UniProt and EGA updates Schema changes (All Species) ---------------------------- ~ Schema changes for structural variations * Add a structural_variation_feature table: store the coordinates * Modification of the structural_variation table: remove the coordinates ~ Additional enum in variation source table for LSDBs Web display updates (All Species) --------------------------------- ~ For the variation displays, we will add more detail to the consequence table, including displays showing the DNA sequence change and amino acid changes. ~ Add a variation annotation panel in the Gene section update consequences for transcript alleles (Human and Mouse) ------------------------------------------------------------ update human and mouse variation transcript alleles due to new gene builds Structural variation (Dog, Human, Mouse and Pig) ------------------------------------------------ ~ Update structural variation data from DGVa for Human, Mouse, Dog and Pig. ~ Add COSMIC structural variation data (Human). From dstaines at ebi.ac.uk Tue Jul 19 15:55:20 2011 From: dstaines at ebi.ac.uk (Dan Staines) Date: Tue, 19 Jul 2011 15:55:20 +0100 Subject: [ensembl-announce] Ensembl Genomes Release 11 Intentions Message-ID: <4E259AD8.9010608@ebi.ac.uk> Dear all, Please find attached a summary of our intentions for release 11 of Ensembl Genomes, due out on 27th September 2011. Please note these are intentions and are therefore not guaranteed to be completed for September. These can also be viewed online at: http://ensemblgenomes.org/info/release11 Best regards, Dan Staines, on behalf of the Ensembl Genomes team. Ensembl Genomes Release 11 Intentions ------------------------------------- General - release scheduled for 27th September 2011 - update to Ensembl 64 software - new Pan Compara database - updated pan concern databases from Ensembl Metazoa - addition of Amphimedon queenslandica, a demosponge from the Great Barrier Reef - update of Drosophila melanogaster gene set and cross-references - update of Drosophila pseudoobscura gene set and cross-references - update of Anopheles gambiae regulation features - updated peptide compara database - updated biomarts Bacteria - no significant updates planned Protists - update of EST and protein feature mapping for diatoms - update of GO annotation sources for Leishmania major - add PHI-base crossreferences to Pythium ultimum and Phytopthora spp - updated biomarts Fungi - addition of Mycosphaerella graminicola, a wheat pathogen - addition of Phaeosphaeria nodorum (aka Stagonospora nodorum), another wheat pathogen - addition of Tuber melanosporum (Perigord Truffle) - update of Schizosaccharomyces pombe gene annotation set - new variation database for Gibberella zeae - add PHI-base crossreferences mapping to Fusarium oxysporum, Gibberella zeae and Gibberella moniliformis - update of the Aspergillus niger crossreferences and protein features - update of the S. cerevisiae crossreferences - add DNA alignments for Nectria haematococca against Fusarium oxysporum, Gibberella zeae and Gibberella moniliformis - updated peptide compara database - updated biomarts Plants - addition of genome for Chlamydomonas reinhardtii - addition of genome for Selaginella moellendorffii - addition of genome for Glycine max - update to assembly for Oryza glaberimma - update to gene models for Vitis vinifera - minor update to cross-references for Arabidopsis thaliana - incorporation of latest Arabidopsis thaliana 1001 genomes variation data - updated DNA compara database - updated peptide compara database - updated gene and variation BioMarts -- Dan Staines, PhD Ensembl Genomes Technical Coordinator EMBL-EBI Tel: +44-(0)1223-492507 Wellcome Trust Genome Campus Fax: +44-(0)1223-494468 Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/ From rhoda at ebi.ac.uk Tue Jul 5 08:28:43 2011 From: rhoda at ebi.ac.uk (Rhoda Kinsella) Date: Tue, 5 Jul 2011 08:28:43 +0100 Subject: [ensembl-announce] Ensembl release 63 Message-ID: The Ensembl project is pleased to announce release 63 of Ensembl (http://www.ensembl.org ) which was released on June 30th. Highlights include a new high-coverage assembly for microbat (Myotis lucifugus), the most recent human and zebrafish manual gene annotations from HAVANA and a fresh update of mouse variation data, among numerous other additions. For more information about this release visit: http://www.ensembl.org/info/website/news.html For the latest news on the ensembl project visit our blog at http://www.ensembl.info The release blog post can be viewed here: http://www.ensembl.info/blog/2011/06/30/ensembl-63-is-out Regards Rhoda Kinsella Rhoda Kinsella Ph.D. Ensembl Bioinformatician, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK. From st3 at sanger.ac.uk Wed Jul 6 10:35:35 2011 From: st3 at sanger.ac.uk (Stephen Trevanion) Date: Wed, 06 Jul 2011 10:35:35 +0100 Subject: [ensembl-announce] ensembl archive website downtime Message-ID: <4E142C67.8010000@sanger.ac.uk> Dear all, The ensembl archive websites will be unavailable for a period of a few hours starting from 10am BST on Fri 8th July. This is required for some essential hardware maintenance. We apologise for any inconvenience this might cause. Steve Trevanion From jeff at ebi.ac.uk Tue Jul 12 15:07:15 2011 From: jeff at ebi.ac.uk (Jeff Almeida-King) Date: Tue, 12 Jul 2011 15:07:15 +0100 Subject: [ensembl-announce] Ensembl Genomes release 10 Message-ID: <4E1C5513.6020405@ebi.ac.uk> The Ensembl Genomes Project is pleased to announce release 10 of Ensembl Genomes. The main highlights of this release are: * Software migration to Ensembl 63 * /Trypanosoma brucei/, a causative agent of Human African trypanosomiasis, or sleeping sickness genome added to Ensembl Protists . * /Ustilago maydis/ (Plant-pathogen interaction model)/, //Puccinia triticina /(wheat rust fungus) and /Nectria haematococca / (Plant pathogen) added to Ensembl Fungi. * Latest 1001 Genomes release included for /Arabidopsis thaliana, /together with 5 additional gene models from TAIR10. Projection of GO terms from /Arabidopsis thaliana/ and /Oryza sativa japonica/ to other species based on homology, also added for Ensembl Plants . -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: jeff.vcf Type: text/x-vcard Size: 290 bytes Desc: not available URL: From mr6 at sanger.ac.uk Wed Jul 13 14:35:48 2011 From: mr6 at sanger.ac.uk (Magali Ruffier) Date: Wed, 13 Jul 2011 14:35:48 +0100 Subject: [ensembl-announce] Intentions for Ensembl Release 64 Message-ID: <4E1D9F34.1080101@sanger.ac.uk> An HTML attachment was scrubbed... URL: From mr6 at sanger.ac.uk Fri Jul 15 09:05:21 2011 From: mr6 at sanger.ac.uk (Magali Ruffier) Date: Fri, 15 Jul 2011 09:05:21 +0100 Subject: [ensembl-announce] Intentions for Ensembl Release 64 Message-ID: <4E1FF4C1.4080409@sanger.ac.uk> Hi, Please see below a list of intentions declared for Ensembl release 64 (scheduled for September). Please not that these are intentions and are not guaranteed to be in the release. Thanks, Magali ======================================= Declarations of Intentions - Ensembl 64 ======================================= Compara ======= Pairwise alignments (All Species) --------------------------------- ~ human vs cow lastz alignments ~ human vs tasmanian devil lastz alignments ~ human haplotype alignments for high coverage blastz-net alignments ~ human vs lamprey tblat alignments ~ lamprey vs Ciona intestinalis tblat alignments ~ lamprey vs Danio rerio tblat alignments ~ lamprey vs Gasterosteus aculeatus tblat alignments Multiple alignments (All Species) --------------------------------- ~ 12way-mammal EPO alignments to incorporate new cow ~ 19way-amniota Pecan alignments to incorporate new cow ~ 35way-mammal low-coverage-EPO alignments (new cow) Syntenies (All Species) ----------------------- ~ human-cow synteny ProteinTrees and homologies (All Species) ----------------------------------------- GeneTrees (protein-coding) with new/updated genebuilds and assemblies ~ Clustering using hcluster_sg ~ Multiple sequence alignments using MCoffee without the exon-disaligner module, or Mafft ~ Phylogenetic reconstruction using TreeBeST ~ Homology inference including the recent 'possible_ortholog','putative gene split' and 'contiguous gene split' exceptions ~ Pairwise gene-based dN/dS scores for high coverage species pairs only (both on orthologues and paralogues) ~ GeneTree stable ID mapping ncRNAtrees and homologies (All Species) --------------------------------------- ~ Classification based on Rfam model ~ Multiple sequence alignments with infernal ~ Phylogenetic reconstruction using RaxML ~ Phylogenetic reconstruction using FastTree2 and RaxML-light for very big families ~ Additional multiple sequence alignments with Prank (w/ genomic flanks) ~ Additional phylogenetic reconstruction using PhyML and NJ ~ Phylogenetic tree merging using TreeBeST ~ Homology inference Protein Families (All Species) ------------------------------ Updated MCL families including all Ensembl transcript isoforms and newest Uniprot Metazoa. ~ Clustering by MCL ~ Multiple Sequence Alignments with MAFFT ~ Family stable ID mapping Compara dumps (All Species) --------------------------- ~ EMF dumps for 20 way PECAN multiple aligments ~ BED files for 20 way GERP constrained elements ~ EMF dumps for 12 way EPO multiple aligments ~ EMF dumps for 35 way low-coverage alignments ~ BED files for 35 way low-coverage alignments ~ Data dumps for ProteinTrees ~ Data dumps for ncRNAtrees API/schema changes (All Species) -------------------------------- ~ changes in the class hierarchy (NestedSet-Member-AlignedMember) to achieve better flexibility and fight code redundancy ~ possible changes in the schema: adding a new "header" table for a tree root, moving general properties of the tree into that table ~ possible changes in the schema: adding tables for tree's properties and node's properties to make tag storage and extraction more efficient Core ==== Xref projections (All Species) ------------------------------ Project GO IDs and gene names to species. Xrefs (All Species) ------------------- Update xrefs for human, mouse, sea squirt ciona intestinalis and ciona savignyi, madagascar hedgehog, western european hedgehog, mouse lemur, platypus, bushbaby, shrew, squirrel schema change (All Species) --------------------------- is_ref will be added to the alt_allele table to show which is the reference gene. Embl/ Genbank flat file dumps (All Species) ------------------------------------------- Schema version update (All Species) ----------------------------------- patch_63_64_a.sql update schema version to 64 LRG import (Human) ------------------ Import of new LRG sequences Funcgen ======= New Regulatory Data (Human and Mouse) ------------------------------------- ~ New Mouse MEL cell-line regulatory build, including Dnase-Seq, and ChIP-Seq for p300, cMyb, USF2, Rad21, NELFe and Max. All data is from ENCODE, following their data policies. ~ New Human CD4 ChIP-Seq data for CBP, p300, MOF, PCAF, Tip60, HDAC1, HDAC2, HDAC3 and HDAC6 (Wang et al, 2009). A new regulatory build was made to incorporate this data. MotifFeatures: Scores Rounded (All Species) ------------------------------------------- MotifFeature scores were rounded to 3 decimal places. MicroArray Mapping (Human, Mouse and Rat) ----------------------------------------- Micro array mapping has been performed for those species with new assemblies or updated gene builds. DNA methylation DAS tracks (Human) ---------------------------------- We have updated the set of DNA methylation DAS tracks using data available from the ENCODE project. patch_63_64_a - Schema version (All Species) -------------------------------------------- The schema_cersion entry in the meta table has been patched to version 64. patch_63_64_b - Cell type experimental factor ontology ID (All Species) ----------------------------------------------------------------------- The cell_type table has had an efo_id field added to represent links to the Experimental Factor Ontology. patch_63_64_c - Experimental meta data (All Species) ---------------------------------------------------- A patch has been applied to add fields to capture experimental meta data e.g. archive & pubmed IDs Genebuild ========= Lamprey genome (Lamprey) ------------------------ A full annotated gene set for the lamprey genome Human cDNA update (Human) ------------------------- New cDNA db for human. GRCh37.p5 (Human) ----------------- Adding the fifth patch release for the human assembly. This alters the assembly information in all human databases. GRCh37.p5 annotation (Human) ---------------------------- Annotation of the patches in the other features db, including projection of annotation from the primary assembly. Cow genebuild (Cow) ------------------- A new genebuild has been done on the cow UMD 3.1 assembly. A new otherfeatures database has also been prepared. Mouse gene set update (Mouse) ----------------------------- The merged gene set has been updated to incorporate the latest Vega manual annotation. Tasmanian Devil Genome (Tasmanian devil) ---------------------------------------- A genebuild on the Tasmanian Devil 7.0 assembly has been created along with an otherfeatures database containing RNASeq models. Update to Ensembl-Havana GENCODE gene set (release 9) (Human) ------------------------------------------------------------- Update to Ensembl-Havana GENCODE gene set (release 9) based on Ensembl gene set and latest Havana gene annotation. GENCODE RNA-Seq (Human) ----------------------- ----------------------- Human Vega annotation (Human) ----------------------------- Manual annotation of human from Havana has been updated. This represents the annotation presented in Vega release 44. Annotation by Havana of chromosome 14 has been completed. Mouse Vega annotation (Mouse) ----------------------------- Manual annotation of mouse from Havana has been updated, including annotation of the MHC region on chromosome 17. The data represents the annotation presented in Vega release 44. Mouse cDNA update (Mouse) ------------------------- The latest set of cDNAs for mouse (as of dd/mon/yyyy) from the European Nucleotide Archive and NCBI RefSeq were aligned to the current genome using Exonerate.There are nnnn new cDNA for Ensembl 64. Flagging obsolete Uniprot proteins (All Species) ------------------------------------------------ Flag the obsolete proteins in Uniprot used as supporting evidence Flagging obsolete Ensembl proteins (All Species) ------------------------------------------------ Flag obsolete human Ensembl proteins used as supporting evidence Gorilla 3.1 projection (Gorilla) -------------------------------- A new AGP file has been provided for gorilla, using the same contigs but with different gaps sizes. Genes from the e63 release will be projected onto the updated assembly. Removal of ambiguous bases from Takifugu rubripes (Fugu) -------------------------------------------------------- Removed the 'R' and 'Y' ambiguous bases from scaffold_20 in takifugu_rubripes_core_64_4. Mart ==== Ensembl 64 mart databases (All Species) --------------------------------------- Full build of all seven marts for release 64 Variation ========= dbSNP 133 import (Cow) ---------------------- dbSNP Build 133 for cow based on the UMD_3.1 assembly. LRG variant import (Human) -------------------------- variants on LRG sequences Phenotype annotations (Human) ----------------------------- ~ COSMIC import update. Minor changes in COSMIC sample names ~ OMIM, NHGRI GWAS catalog, UniProt and EGA updates Schema changes (All Species) ---------------------------- ~ Schema changes for structural variations * Add a structural_variation_feature table: store the coordinates * Modification of the structural_variation table: remove the coordinates ~ Additional enum in variation source table for LSDBs Web display updates (All Species) --------------------------------- ~ For the variation displays, we will add more detail to the consequence table, including displays showing the DNA sequence change and amino acid changes. ~ Add a variation annotation panel in the Gene section update consequences for transcript alleles (Human and Mouse) ------------------------------------------------------------ update human and mouse variation transcript alleles due to new gene builds Structural variation (Dog, Human, Mouse and Pig) ------------------------------------------------ ~ Update structural variation data from DGVa for Human, Mouse, Dog and Pig. ~ Add COSMIC structural variation data (Human). From dstaines at ebi.ac.uk Tue Jul 19 15:55:20 2011 From: dstaines at ebi.ac.uk (Dan Staines) Date: Tue, 19 Jul 2011 15:55:20 +0100 Subject: [ensembl-announce] Ensembl Genomes Release 11 Intentions Message-ID: <4E259AD8.9010608@ebi.ac.uk> Dear all, Please find attached a summary of our intentions for release 11 of Ensembl Genomes, due out on 27th September 2011. Please note these are intentions and are therefore not guaranteed to be completed for September. These can also be viewed online at: http://ensemblgenomes.org/info/release11 Best regards, Dan Staines, on behalf of the Ensembl Genomes team. Ensembl Genomes Release 11 Intentions ------------------------------------- General - release scheduled for 27th September 2011 - update to Ensembl 64 software - new Pan Compara database - updated pan concern databases from Ensembl Metazoa - addition of Amphimedon queenslandica, a demosponge from the Great Barrier Reef - update of Drosophila melanogaster gene set and cross-references - update of Drosophila pseudoobscura gene set and cross-references - update of Anopheles gambiae regulation features - updated peptide compara database - updated biomarts Bacteria - no significant updates planned Protists - update of EST and protein feature mapping for diatoms - update of GO annotation sources for Leishmania major - add PHI-base crossreferences to Pythium ultimum and Phytopthora spp - updated biomarts Fungi - addition of Mycosphaerella graminicola, a wheat pathogen - addition of Phaeosphaeria nodorum (aka Stagonospora nodorum), another wheat pathogen - addition of Tuber melanosporum (Perigord Truffle) - update of Schizosaccharomyces pombe gene annotation set - new variation database for Gibberella zeae - add PHI-base crossreferences mapping to Fusarium oxysporum, Gibberella zeae and Gibberella moniliformis - update of the Aspergillus niger crossreferences and protein features - update of the S. cerevisiae crossreferences - add DNA alignments for Nectria haematococca against Fusarium oxysporum, Gibberella zeae and Gibberella moniliformis - updated peptide compara database - updated biomarts Plants - addition of genome for Chlamydomonas reinhardtii - addition of genome for Selaginella moellendorffii - addition of genome for Glycine max - update to assembly for Oryza glaberimma - update to gene models for Vitis vinifera - minor update to cross-references for Arabidopsis thaliana - incorporation of latest Arabidopsis thaliana 1001 genomes variation data - updated DNA compara database - updated peptide compara database - updated gene and variation BioMarts -- Dan Staines, PhD Ensembl Genomes Technical Coordinator EMBL-EBI Tel: +44-(0)1223-492507 Wellcome Trust Genome Campus Fax: +44-(0)1223-494468 Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/