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EBI
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Genome resources at EMBL-EBI: Ensembl and Ensembl Genomes
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EBI
Event: Plant and Animal Genomes Conference 2012. Speaker: Bert Overduin The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) provides a comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. Major components of ENA include the Sequence Read Archive (SRA) for next generation data and EMBL-Bank for assembled and annotated sequences. ENA works closely together with NCBI and DDBJ as partners in the International Nucleotide Sequence Database Collaboration (INSDC). Data arrive at ENA from a variety of sources. These include submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centres and routine and comprehensive exchange with our INSDC partners. Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and provides a portfolio of interactive and programmatic submission services to ensure the smoothest flow possible of data into the public domain. ENA data can be searched using rapid sequence similarity and text search services provided both within web-based tools and under programmatic interfaces. Data can be retrieved in a variety of appropriate widely adopted formats through a web browser and extensive REST services. This presentation will consist of an introduction to ENA, followed by a short demonstration of the various ways data can be browsed and retrieved.
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Automatic Annotation in UniProtKB
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EBI
Event: Plant and Animal Genomes conference 2012 Speaker: Sandra Orchard InterPro is an open-source protein resource used for the automatic annotation of proteins, and is scalable to the analysis of entire new genomes through the use of a downloadable version of InterProScan, which can be incorporated into an existing local pipeline. InterPro integrates protein signatures from 11 major signature databases (CATH-Gene3D, HAMAP, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY, and TIGRFAMs) into a single resource, taking advantage of the different areas of specialization of each to produce a resource that provides protein classification on multiple levels: protein families, structural superfamilies and functionally close subfamilies, as well as functional domains, repeats and important sites. The InterPro website has been improved, following extensive community consultation and a new version of InterProScan promises improved speed, ease of implementation as well as additional functionalities.
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EBI
Event: Plant and Animal Genomes conference Speaker: Jane Loveland (Wellcome Trust Sanger Institute The Human and Vertebrate Analysis and Annotation (HAVANA) team at the Wellcome Trust Sanger Institute (WTSI) undertakes manual annotation of finished vertebrate genomic sequence. This annotation is available from the Vertebrate Genome Annotation database (VEGA) (http://vega.sanger.ac.uk) and is in progress for whole genomes (human, mouse and zebrafish) and specific regions of interest, such as pig (SLA and LRC), dog (DLA), wallaby (MHC), gorilla (MHC and LRC). Manual annotation of genomic data is extremely valuable to produce an accurate reference gene set but is expensive compared with automatic methods and so has been limited to model organisms. Annotation tools that have been developed at the Wellcome Trust Sanger Institute are being used to fill that gap, as they can be used remotely and so open up viable community annotation collaborations. We introduce the “Blessed” annotator and “Gatekeeper” approach to Community Annotation using the Otterlace/ZMap genome annotation tool. We also describe the strategies adopted for annotation consistency, quality control and viewing of the annotation. We are currently involved in the annotation of immune response genes in pig and have annotated over 1700 genes in a community annotation effort, together with the sequencing and annotation of pig chromosomes X and Y at WTSI that will be displayed on the VEGA website. Presented on behalf of the HAVANA team, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs UK.
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EBI
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