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      InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

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          Abstract

          The InParanoid project gathers proteomes of completely sequenced eukaryotic species plus Escherichia coli and calculates pairwise ortholog relationships among them. The new release 7.0 of the database has grown by an order of magnitude over the previous version and now includes 100 species and their collective 1.3 million proteins organized into 42.7 million pairwise ortholog groups. The InParanoid algorithm itself has been revised and is now both more specific and sensitive. Based on results from our recent benchmarking of low-complexity filters in homology assignment, a two-pass BLAST approach was developed that makes use of high-precision compositional score matrix adjustment, but avoids the alignment truncation that sometimes follows. We have also updated the InParanoid web site ( http://InParanoid.sbc.su.se). Several features have been added, the response times have been improved and the site now sports a new, clearer look. As the number of ortholog databases has grown, it has become difficult to compare among these resources due to a lack of standardized source data and incompatible representations of ortholog relationships. To facilitate data exchange and comparisons among ortholog databases, we have developed and are making available two XML schemas: SeqXML for the input sequences and OrthoXML for the output ortholog clusters.

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          Distinguishing homologous from analogous proteins.

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            The Arabidopsis Information Resource (TAIR): gene structure and function annotation

            The Arabidopsis Information Resource (TAIR, http://arabidopsis.org) is the model organism database for the fully sequenced and intensively studied model plant Arabidopsis thaliana. Data in TAIR is derived in large part from manual curation of the Arabidopsis research literature and direct submissions from the research community. New developments at TAIR include the addition of the GBrowse genome viewer to the TAIR site, a redesigned home page, navigation structure and portal pages to make the site more intuitive and easier to use, the launch of several TAIR web services and a new genome annotation release (TAIR7) in April 2007. A combination of manual and computational methods were used to generate this release, which contains 27 029 protein-coding genes, 3889 pseudogenes or transposable elements and 1123 ncRNAs (32 041 genes in all, 37 019 gene models). A total of 681 new genes and 1002 new splice variants were added. Overall, 10 098 loci (one-third of all loci from the previous TAIR6 release) were updated for the TAIR7 release.
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              Ensembl 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/).
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                Author and article information

                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                nar
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                January 2010
                5 November 2009
                5 November 2009
                : 38
                : Database issue , Database issue
                : D196-D203
                Affiliations
                Department of Biochemistry and Biophysics, Stockholm Bioinformatics Centre, AlbaNova University Centre, Stockholm University, SE-10691 Stockholm, Sweden
                Author notes
                *To whom correspondence should be addressed. Tel: +4685 537 8566; Fax: +4685 537 8214; Email: gabriel.ostlund@ 123456sbc.su.se

                The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

                Present address: Tina Köstler, Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, Dr Bohr Gasse 9, A-1030 Wien, Austria.

                Article
                gkp931
                10.1093/nar/gkp931
                2808972
                19892828
                68ad7ca4-c0ae-4817-88fb-55117b8bd20f
                © The Author(s) 2009. Published by Oxford University Press.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 15 September 2009
                : 7 October 2009
                : 8 October 2009
                Categories
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                Genetics
                Genetics

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