From dstaines at ebi.ac.uk Tue Jun 12 16:16:02 2012 From: dstaines at ebi.ac.uk (Dan Staines) Date: Tue, 12 Jun 2012 16:16:02 +0100 Subject: [ensembl-announce] Ensembl Genomes Release 15 Intentions Message-ID: <4FD75D32.5040803@ebi.ac.uk> Dear all, Please find attached a summary of our intentions for release 15 of Ensembl Genomes, due out on 7th August 2012. Please note these are intentions and are therefore not guaranteed to be completed for August. These can also be viewed online at: http://ensemblgenomes.org/info/release15 Best regards, Dan Staines, on behalf of the Ensembl Genomes team. Ensembl Genomes Release 15 Intentions General - release scheduled for 7th August 2012 - update to Ensembl 68 software Metazoa - Update to the cross-references for the mosquitoes (Aedes aegypti, Culex quinquefasciatus and Anopheles gambiae) and the tick (Ixodes scapularis). - Updated variation data for Anopheles gambiae. - Update to BioMart to include new cross-references and new variation data. Bacteria - update to peptide compara to address some minor interface problems Protists - Alignment of RNA-Seq data from the ENA Sequence Read Archive to the genomes of Phytophthora infestans, Phytophthora sojae and Albugo laibachii. Fungi - Addition of the genome for Leptosphaeria maculans, including alignment of data from dbEST and alignment of the oligo array GSE27152. - New assembly for Botryotinia fuckeliana. - Addition of variation data for Puccinia graminis. - Addition of simple repeat data for Puccinia graminis. - Addition of rRNA repeat data for Saccharomyces cerevisiae. - Addition of PHIbase cross-references and phenotype data for Magnaporthe oryzae. - Alignment of RNA-Seq data from the ENA Sequence Read Archive to the genome of Fusarium oxysporum. - Update of protein features for Fusarium oxysporum from InterPro. - Update to peptide comparative genomes database to include new and updated gene models. - Update to BioMart to include the new and updated data described above. Plants - Inclusion of structural variation from dGVA for Sorghum bicolor. - Minor update to variation dataset for Zea mays. - Updated BioMart to include variation changes for Zea mays. - Alignment of wheat SNPs from the A, B and D genomes to Brachypodium distachyon. - Minor updates to internal representation of assemblies for Brassica rapa, Arabidopsis thaliana, and Vitis vinifera (overall assemblies remains unchanged). -- 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 Mon Jun 18 14:20:10 2012 From: st3 at sanger.ac.uk (Stephen Trevanion) Date: Mon, 18 Jun 2012 14:20:10 +0100 Subject: [ensembl-announce] BLAST / BLAT unavailable 20th June Message-ID: <4FDF2B0A.3070103@sanger.ac.uk> BLAST and BLAT will be unavailable for a short period from 13.00 BST on Wed 20th June due to some hardware maintenance being required. We expect this work to be complete within the hour. This will affect the main Ensembl site and the mirror sites. Apologies for any incovenience caused. Steve From dstaines at ebi.ac.uk Tue Jun 12 16:16:02 2012 From: dstaines at ebi.ac.uk (Dan Staines) Date: Tue, 12 Jun 2012 16:16:02 +0100 Subject: [ensembl-announce] Ensembl Genomes Release 15 Intentions Message-ID: <4FD75D32.5040803@ebi.ac.uk> Dear all, Please find attached a summary of our intentions for release 15 of Ensembl Genomes, due out on 7th August 2012. Please note these are intentions and are therefore not guaranteed to be completed for August. These can also be viewed online at: http://ensemblgenomes.org/info/release15 Best regards, Dan Staines, on behalf of the Ensembl Genomes team. Ensembl Genomes Release 15 Intentions General - release scheduled for 7th August 2012 - update to Ensembl 68 software Metazoa - Update to the cross-references for the mosquitoes (Aedes aegypti, Culex quinquefasciatus and Anopheles gambiae) and the tick (Ixodes scapularis). - Updated variation data for Anopheles gambiae. - Update to BioMart to include new cross-references and new variation data. Bacteria - update to peptide compara to address some minor interface problems Protists - Alignment of RNA-Seq data from the ENA Sequence Read Archive to the genomes of Phytophthora infestans, Phytophthora sojae and Albugo laibachii. Fungi - Addition of the genome for Leptosphaeria maculans, including alignment of data from dbEST and alignment of the oligo array GSE27152. - New assembly for Botryotinia fuckeliana. - Addition of variation data for Puccinia graminis. - Addition of simple repeat data for Puccinia graminis. - Addition of rRNA repeat data for Saccharomyces cerevisiae. - Addition of PHIbase cross-references and phenotype data for Magnaporthe oryzae. - Alignment of RNA-Seq data from the ENA Sequence Read Archive to the genome of Fusarium oxysporum. - Update of protein features for Fusarium oxysporum from InterPro. - Update to peptide comparative genomes database to include new and updated gene models. - Update to BioMart to include the new and updated data described above. Plants - Inclusion of structural variation from dGVA for Sorghum bicolor. - Minor update to variation dataset for Zea mays. - Updated BioMart to include variation changes for Zea mays. - Alignment of wheat SNPs from the A, B and D genomes to Brachypodium distachyon. - Minor updates to internal representation of assemblies for Brassica rapa, Arabidopsis thaliana, and Vitis vinifera (overall assemblies remains unchanged). -- 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 Mon Jun 18 14:20:10 2012 From: st3 at sanger.ac.uk (Stephen Trevanion) Date: Mon, 18 Jun 2012 14:20:10 +0100 Subject: [ensembl-announce] BLAST / BLAT unavailable 20th June Message-ID: <4FDF2B0A.3070103@sanger.ac.uk> BLAST and BLAT will be unavailable for a short period from 13.00 BST on Wed 20th June due to some hardware maintenance being required. We expect this work to be complete within the hour. This will affect the main Ensembl site and the mirror sites. Apologies for any incovenience caused. Steve