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      • Record: found
      • Abstract: found
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      Ensembl 2012

      research-article
      Author(s): 1 , 2 , * , 2 , 2 , 1 , 2 , 1 , 2 , 2 ,   2 , 1 , 1 , 1 , 2 , 2 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 2 , 2 , 1 , 2 , 1 , 1 , 2 , 1 , 2 , 1 , 2 , 2 , 1 , 2 , 1 , 1 , 1 , 2 , 1 , 2 , 1 , 2 , 2 , 1 , 1 , 2 , 1 , 2 , 2
      Publication date (Electronic):
      Journal: Nucleic Acids Research
      Publisher: Oxford University Press

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          Abstract

          The Ensembl project ( http://www.ensembl.org) provides genome resources for chordate genomes with a particular focus on human genome data as well as data for key model organisms such as mouse, rat and zebrafish. Five additional species were added in the last year including gibbon ( Nomascus leucogenys) and Tasmanian devil ( Sarcophilus harrisii) bringing the total number of supported species to 61 as of Ensembl release 64 (September 2011). Of these, 55 species appear on the main Ensembl website and six species are provided on the Ensembl preview site (Pre!Ensembl; http://pre.ensembl.org) with preliminary support. The past year has also seen improvements across the project.

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          • Record: found
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          The Universal Protein Resource (UniProt) in 2010

          emmanuel boutet, Claire O'Donovan, Amos Bairoch (2009)
          The primary mission of UniProt is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. UniProt is produced by the UniProt Consortium which consists of groups from the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. UniProt is updated and distributed every 3 weeks and can be accessed online for searches or download at http://www.uniprot.org.
          Article 0 comments Cited 498 times – based on 0 reviews     Review now
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            The UCSC Genome Browser database: update 2011

            Pauline Fujita, Brooke Rhead, Ann Zweig … (2010)
            The University of California, Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online access to a database of genomic sequence and annotation data for a wide variety of organisms. The Browser also has many tools for visualizing, comparing and analyzing both publicly available and user-generated genomic data sets, aligning sequences and uploading user data. Among the features released this year are a gene search tool and annotation track drag-reorder functionality as well as support for BAM and BigWig/BigBed file formats. New display enhancements include overlay of multiple wiggle tracks through use of transparent coloring, options for displaying transformed wiggle data, a ‘mean+whiskers’ windowing function for display of wiggle data at high zoom levels, and more color schemes for microarray data. New data highlights include seven new genome assemblies, a Neandertal genome data portal, phenotype and disease association data, a human RNA editing track, and a zebrafish Conservation track. We also describe updates to existing tracks.
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              Ensembl 2009

              T. J. P. Hubbard, B. L. Aken, S. Ayling … (2009)
              The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases, and other information for chordate, selected model organism and disease vector genomes. As of release 51 (November 2008), Ensembl fully supports 45 species, and three additional species have preliminary support. New species in the past year include orangutan and six additional low coverage mammalian genomes. Major additions and improvements to Ensembl since our previous report include a major redesign of our website; generation of multiple genome alignments and ancestral sequences using the new Enredo-Pecan-Ortheus pipeline and development of our software infrastructure, particularly to support the Ensembl Genomes project (http://www.ensemblgenomes.org/).
              Article 0 comments Cited 366 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Journal ID (hwp): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date Collection: January 2012
                Publication date (Print): January 2012
                Publication date (Electronic): 15 November 2011
                Publication date PMC-release: 15 November 2011
                Volume: 40
                Issue: D1 , Database issue
                Pages: D84-D90
                Affiliations
                1European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK and 2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
                Author notes
                *To whom correspondence should be addressed. Tel: +44 1223 492581; Fax: +44 1223 494494; Email: flicek@ 123456ebi.ac.uk
                Article
                Publisher ID: gkr991
                DOI: 10.1093/nar/gkr991
                PMC ID: 3245178
                PubMed ID: 22086963
                SO-VID: 099446e5-9321-4d57-b22d-c035bc7713e8
                Copyright © © The Author(s) 2011. Published by Oxford University Press.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 10 October 2011
                Date accepted : 17 October 2011
                Page count
                Pages: 7
                Categories
                Subject: Articles

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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