From ap5 at sanger.ac.uk Tue Nov 9 16:09:45 2010 From: ap5 at sanger.ac.uk (Anne Parker) Date: Tue, 9 Nov 2010 16:09:45 +0000 Subject: [ensembl-announce] Ensembl Release 60 Message-ID: The Ensembl project is pleased to announce release 60 of Ensembl (http://www.ensembl.org/ ). Highlights of this release are: * New species - Giant Panda * New assemblies and genebuilds for zebrafish and rabbit * New display for GO terms * Improved navigation on Region in Detail, including autocompletion of gene display names (e.g. HGNC) For more information visit: http://www.ensembl.org/info/website/news/index.html For the latest news on the Ensembl project, visit our blog at http://ensembl.blogspot.com Anne Parker Ensembl Web Production Manager http://www.ensembl.org From glenn at ebi.ac.uk Wed Nov 10 16:27:06 2010 From: glenn at ebi.ac.uk (Glenn Proctor) Date: Wed, 10 Nov 2010 16:27:06 +0000 Subject: [ensembl-announce] US East coast Ensembl mirror now available Message-ID: We are pleased to announce the public availability of a second Ensembl mirror in the USA. This can be found at http://useast.ensembl.org/ . This provides a fully functional Ensembl website, but there are some things to note which I've listed below. REDIRECTION We don't automatically redirect users to the new mirror, although we have plans for this in future. So for now you'll need to explicitly visit http://useast.ensembl.org/ to access it. USER LOGINS If you use the login functionality, your existing login will work on http://useast.ensembl.org/ , although configuration changes will not be reflected between sites. We plan to support shared logins very soon. OTHER SERVICES We don't yet offer the Biomart or BLAST/BLAT services on the new mirror; these will come in the near future. We currently have no plans to offer a US-based MySQL mirror, so you should continue use ensembldb.ensembl.org for MySQL queries. We're very keen to hear your experiences with this new mirror, particularly from our US users, please use the Helpdesk (http://www.ensembl.org/Help/Contact) in the first instance, or contact me directly. We also have advanced plans for mirrors in other parts of the world, so stay tuned! Glenn. From dstaines at ebi.ac.uk Fri Nov 19 12:11:25 2010 From: dstaines at ebi.ac.uk (Dan Staines) Date: Fri, 19 Nov 2010 12:11:25 +0000 Subject: [ensembl-announce] Ensembl Genomes Release 7 Intentions In-Reply-To: <4C987B22.3060404@ebi.ac.uk> References: <4C987B22.3060404@ebi.ac.uk> Message-ID: <4CE6696D.6090404@ebi.ac.uk> Dear all, Release 7 of Ensembl Genomes will now be delayed to November 30th. Apologies for any inconvenience. Regards, Dan Staines. -- 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 st3 at sanger.ac.uk Thu Nov 25 17:12:31 2010 From: st3 at sanger.ac.uk (Stephen Trevanion) Date: Thu, 25 Nov 2010 17:12:31 +0000 Subject: [ensembl-announce] Intentions for Ensembl release 61 Message-ID: <4CEE98FF.9000705@sanger.ac.uk> Please see below a summary for the intentions declared for Ensembl 61 (scheduled for 19th January). Note these are intentions and are not guaranteed to be in the release Regards, Steve ------------------------------------------------ Compara: Families- Updated MCL families including all Ensembl transcript isoforms and newest Uniprot Metazoa. * Clustering by MCL * Multiple Sequence Alignments with MAFFT * Family stable ID mapping Gene Homologies- GeneTrees with new/updated genebuilds and assemblies * Updated build of ncRNA trees * Clustering using hcluster_sg * Multiple Sequence Alignments using consistency-based MCoffee meta-aligner * Homology inference including the recent 'possible_ortholog' type and 'putative gene split' and 'contiguous gene split' exceptions * Pairwise gene-based dN/dS calculations for high coverage species pairs only * GeneTree stable ID mapping Pairwise Alignments- Human - Lizard tBlat - net Human - Turkey tBlat net Turkey - Chicken Lastz Lizard - Chicken Lastz Dog - Horse Lastz **Removing chicken - zebrafinch tBlat Chicken - Turkey -Zebrafinch EPO multiple alignment Core: seq region synonyms- New table seq_region_synonym added to allow multiple names for sequence regions. Species: all species external database references- Human, mouse, rat and tree shrew will be updated. GO term and gene name projections- Gene display names and GO terms will be projected from high-coverage species to those with lower coverage. Ontology database- The Ensembl Ontology database will as usual be populated with the latest available versions of the * Gene Ontology (GO) * Sequence Ontology (SO) embl and genbank dumps- Onlt the reference sequence will be dumped in the main directory for embl and genbank. Unique non-reference regions(haplotype/par regions) will now be dumped in a subdirectory and only contain the unique regions. Funcgen: Array Mapping- Array mapping was updated on all species which have had an update to their genome assemblies or gene builds. The probe/set to transcript xrefs were recalculated across all species. Mouse Regulatory Build- The mouse RegulatoryBuild was re-run to re-introduce some data which had been omitted in the previous build. Genebuild: Human cDNA update- Updated set of cDNA alignments to the human genome. Haplotype correction- Correction of an error that added one extra N to the end of the alternative versions of the chromosomes for five of the haplotypes. The altered alternative chromosomes are: HSCHR6_MHC_MANN, HSCHR6_MHC_MCF, HSCHR6_MHC_SSTO, HSCHR4_1 and HSCHR17_1. Species: Human Zebrafish Havana merge- A merge of the zebrafish core gene set with Havana manual annotation. The core gene set has been altered to include missing genes that were lost in e60 due to a problem in gene clustering. GENCODE gene set update (release 6)- Update to the Ensembl/Havana GENCODE gene set using the latest Vega gene set Updates to mouse and human Vega annotation- The Vega annotation for both human and mouse has been updated. This matches the annotation presented in Vega release 41. new rnaseq database- I will provide a new databases which consists of the core tables ; the data will data from the human bodymap project ( rnasesq data ). This is a new database which has not been released before. This was originally planned for e60. mouse cDNA update- mouse cDNA update Zebrafish Vega annotation- Manual annotation of zebrafish from Havana is now present in Ensembl. This represetns the annotation presented in Vega release 40 Mouse gene set update- A merge of Ensembl core gene set and Vega manual annotation. The core gene set has been improved by incorporating new data resources which had become available since the last NCBIM37 genebuild (April 2007), resulting in the correction of existing gene models and the recovery of new mouse genes with human orthologues. A new otherfeatures database is also available. New assembly for lizard- A new assembly for lizard Turkey- The first genebuild for turkey New Canonical Transcript definition- For previous releases, the canonical transcript of a gene has been set to the transcript with the longest translation (for coding genes) or to the transcript with the longest mRNA (for noncoding genes). From release 61, the canonical transcript for human and mouse will now be set to the longest CCDS transcript. Where no CCDS transcript exists for the gene, the longest Ensembl-HAVANA merge transcript will be used. Species: Human, Mouse Removal of ambiguous bases from human DNA sequence- Ambiguous bases have been replaced with 'N' for the following two human contigs: * contig::AF152363.1:1:185763:1. This contig held 28 ambiguous bases: S(4), W(6), M(5), K(4), R(5), Y(4). * contig::AF152364.1:1:170452:1. This contig held 4 ambiguous bases: S(1), W(1), Y(1), K(1). Updated CCDS- Updated CCDS databases for Human and Mouse. Populates other_features with new gene models and serves data for CCDS Public Note DAS track. Mart: Ensembl Marts for release 61- Full build of all 7 marts for all species. Variation: - import dbSNP 132 (human) - import dbSNP for further species if available in time (mouse, rat, zebrafish, cat, opossum) - import new release of HGMD database - corrections to Affymetrix CNV probe data - import PorcineSNP60 BeadChip - update of zebrafish variation consequences for new gene build - variations will now be flagged and retained instead of failed and deleted for species with a new import of dbSNP - produce GVF file dumps of all variants and their consequence by species Wormbase: C.elegans WS220- A new version of the C.elegans database based on the official frozen WS220 WormBase release. From ap5 at sanger.ac.uk Tue Nov 9 16:09:45 2010 From: ap5 at sanger.ac.uk (Anne Parker) Date: Tue, 9 Nov 2010 16:09:45 +0000 Subject: [ensembl-announce] Ensembl Release 60 Message-ID: The Ensembl project is pleased to announce release 60 of Ensembl (http://www.ensembl.org/ ). Highlights of this release are: * New species - Giant Panda * New assemblies and genebuilds for zebrafish and rabbit * New display for GO terms * Improved navigation on Region in Detail, including autocompletion of gene display names (e.g. HGNC) For more information visit: http://www.ensembl.org/info/website/news/index.html For the latest news on the Ensembl project, visit our blog at http://ensembl.blogspot.com Anne Parker Ensembl Web Production Manager http://www.ensembl.org From glenn at ebi.ac.uk Wed Nov 10 16:27:06 2010 From: glenn at ebi.ac.uk (Glenn Proctor) Date: Wed, 10 Nov 2010 16:27:06 +0000 Subject: [ensembl-announce] US East coast Ensembl mirror now available Message-ID: We are pleased to announce the public availability of a second Ensembl mirror in the USA. This can be found at http://useast.ensembl.org/ . This provides a fully functional Ensembl website, but there are some things to note which I've listed below. REDIRECTION We don't automatically redirect users to the new mirror, although we have plans for this in future. So for now you'll need to explicitly visit http://useast.ensembl.org/ to access it. USER LOGINS If you use the login functionality, your existing login will work on http://useast.ensembl.org/ , although configuration changes will not be reflected between sites. We plan to support shared logins very soon. OTHER SERVICES We don't yet offer the Biomart or BLAST/BLAT services on the new mirror; these will come in the near future. We currently have no plans to offer a US-based MySQL mirror, so you should continue use ensembldb.ensembl.org for MySQL queries. We're very keen to hear your experiences with this new mirror, particularly from our US users, please use the Helpdesk (http://www.ensembl.org/Help/Contact) in the first instance, or contact me directly. We also have advanced plans for mirrors in other parts of the world, so stay tuned! Glenn. From dstaines at ebi.ac.uk Fri Nov 19 12:11:25 2010 From: dstaines at ebi.ac.uk (Dan Staines) Date: Fri, 19 Nov 2010 12:11:25 +0000 Subject: [ensembl-announce] Ensembl Genomes Release 7 Intentions In-Reply-To: <4C987B22.3060404@ebi.ac.uk> References: <4C987B22.3060404@ebi.ac.uk> Message-ID: <4CE6696D.6090404@ebi.ac.uk> Dear all, Release 7 of Ensembl Genomes will now be delayed to November 30th. Apologies for any inconvenience. Regards, Dan Staines. -- 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 st3 at sanger.ac.uk Thu Nov 25 17:12:31 2010 From: st3 at sanger.ac.uk (Stephen Trevanion) Date: Thu, 25 Nov 2010 17:12:31 +0000 Subject: [ensembl-announce] Intentions for Ensembl release 61 Message-ID: <4CEE98FF.9000705@sanger.ac.uk> Please see below a summary for the intentions declared for Ensembl 61 (scheduled for 19th January). Note these are intentions and are not guaranteed to be in the release Regards, Steve ------------------------------------------------ Compara: Families- Updated MCL families including all Ensembl transcript isoforms and newest Uniprot Metazoa. * Clustering by MCL * Multiple Sequence Alignments with MAFFT * Family stable ID mapping Gene Homologies- GeneTrees with new/updated genebuilds and assemblies * Updated build of ncRNA trees * Clustering using hcluster_sg * Multiple Sequence Alignments using consistency-based MCoffee meta-aligner * Homology inference including the recent 'possible_ortholog' type and 'putative gene split' and 'contiguous gene split' exceptions * Pairwise gene-based dN/dS calculations for high coverage species pairs only * GeneTree stable ID mapping Pairwise Alignments- Human - Lizard tBlat - net Human - Turkey tBlat net Turkey - Chicken Lastz Lizard - Chicken Lastz Dog - Horse Lastz **Removing chicken - zebrafinch tBlat Chicken - Turkey -Zebrafinch EPO multiple alignment Core: seq region synonyms- New table seq_region_synonym added to allow multiple names for sequence regions. Species: all species external database references- Human, mouse, rat and tree shrew will be updated. GO term and gene name projections- Gene display names and GO terms will be projected from high-coverage species to those with lower coverage. Ontology database- The Ensembl Ontology database will as usual be populated with the latest available versions of the * Gene Ontology (GO) * Sequence Ontology (SO) embl and genbank dumps- Onlt the reference sequence will be dumped in the main directory for embl and genbank. Unique non-reference regions(haplotype/par regions) will now be dumped in a subdirectory and only contain the unique regions. Funcgen: Array Mapping- Array mapping was updated on all species which have had an update to their genome assemblies or gene builds. The probe/set to transcript xrefs were recalculated across all species. Mouse Regulatory Build- The mouse RegulatoryBuild was re-run to re-introduce some data which had been omitted in the previous build. Genebuild: Human cDNA update- Updated set of cDNA alignments to the human genome. Haplotype correction- Correction of an error that added one extra N to the end of the alternative versions of the chromosomes for five of the haplotypes. The altered alternative chromosomes are: HSCHR6_MHC_MANN, HSCHR6_MHC_MCF, HSCHR6_MHC_SSTO, HSCHR4_1 and HSCHR17_1. Species: Human Zebrafish Havana merge- A merge of the zebrafish core gene set with Havana manual annotation. The core gene set has been altered to include missing genes that were lost in e60 due to a problem in gene clustering. GENCODE gene set update (release 6)- Update to the Ensembl/Havana GENCODE gene set using the latest Vega gene set Updates to mouse and human Vega annotation- The Vega annotation for both human and mouse has been updated. This matches the annotation presented in Vega release 41. new rnaseq database- I will provide a new databases which consists of the core tables ; the data will data from the human bodymap project ( rnasesq data ). This is a new database which has not been released before. This was originally planned for e60. mouse cDNA update- mouse cDNA update Zebrafish Vega annotation- Manual annotation of zebrafish from Havana is now present in Ensembl. This represetns the annotation presented in Vega release 40 Mouse gene set update- A merge of Ensembl core gene set and Vega manual annotation. The core gene set has been improved by incorporating new data resources which had become available since the last NCBIM37 genebuild (April 2007), resulting in the correction of existing gene models and the recovery of new mouse genes with human orthologues. A new otherfeatures database is also available. New assembly for lizard- A new assembly for lizard Turkey- The first genebuild for turkey New Canonical Transcript definition- For previous releases, the canonical transcript of a gene has been set to the transcript with the longest translation (for coding genes) or to the transcript with the longest mRNA (for noncoding genes). From release 61, the canonical transcript for human and mouse will now be set to the longest CCDS transcript. Where no CCDS transcript exists for the gene, the longest Ensembl-HAVANA merge transcript will be used. Species: Human, Mouse Removal of ambiguous bases from human DNA sequence- Ambiguous bases have been replaced with 'N' for the following two human contigs: * contig::AF152363.1:1:185763:1. This contig held 28 ambiguous bases: S(4), W(6), M(5), K(4), R(5), Y(4). * contig::AF152364.1:1:170452:1. This contig held 4 ambiguous bases: S(1), W(1), Y(1), K(1). Updated CCDS- Updated CCDS databases for Human and Mouse. Populates other_features with new gene models and serves data for CCDS Public Note DAS track. Mart: Ensembl Marts for release 61- Full build of all 7 marts for all species. Variation: - import dbSNP 132 (human) - import dbSNP for further species if available in time (mouse, rat, zebrafish, cat, opossum) - import new release of HGMD database - corrections to Affymetrix CNV probe data - import PorcineSNP60 BeadChip - update of zebrafish variation consequences for new gene build - variations will now be flagged and retained instead of failed and deleted for species with a new import of dbSNP - produce GVF file dumps of all variants and their consequence by species Wormbase: C.elegans WS220- A new version of the C.elegans database based on the official frozen WS220 WormBase release.