دورية أكاديمية
MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life.
| العنوان: | MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life. |
|---|---|
| المؤلفون: | Chorostecki U; Barcelona Supercomputing Centre (BSC-CNS), 08034 Barcelona, Spain.; Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain., Molina M; Barcelona Supercomputing Centre (BSC-CNS), 08034 Barcelona, Spain.; Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain., Pryszcz LP; Centre for Genomic Regulation, 08003 Barcelona, Spain.; International Institute of Molecular and Cell Biology, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland., Gabaldón T; Barcelona Supercomputing Centre (BSC-CNS), 08034 Barcelona, Spain.; Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.; ICREA, 08010 Barcelona, Spain. |
| المصدر: | Nucleic acids research [Nucleic Acids Res] 2020 Jul 02; Vol. 48 (W1), pp. W553-W557. |
| نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't |
| اللغة: | English |
| بيانات الدورية: | Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: 1992- : Oxford : Oxford University Press Original Publication: London, Information Retrieval ltd. |
| مواضيع طبية MeSH: | Multigene Family* , Phylogeny* , Software*, Sequence Homology |
| مستخلص: | Inferring homology relationships across genes in different species is a central task in comparative genomics. Therefore, a large number of resources and methods have been developed over the years. Some public databases include phylogenetic trees of homologous gene families which can be used to further differentiate homology relationships into orthology and paralogy. MetaPhOrs is a web server that integrates phylogenetic information from different sources to provide orthology and paralogy relationships based on a common phylogeny-based predictive algorithm and associated with a consistency-based confidence score. Here we describe the latest version of the web server which includes major new implementations and provides orthology and paralogy relationships derived from ∼8.2 million gene family trees-from 13 different source repositories across ∼4000 species with sequenced genomes. MetaPhOrs server is freely available, without registration, at http://orthology.phylomedb.org/. (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.) |
| References: | Nucleic Acids Res. 2011 Mar;39(5):e32. (PMID: 21149260) Nat Rev Genet. 2013 May;14(5):360-6. (PMID: 23552219) Nucleic Acids Res. 2008 Jan;36(Database issue):D491-6. (PMID: 17962297) Science. 2014 Dec 12;346(6215):1320-31. (PMID: 25504713) Genome Res. 2003 Sep;13(9):2178-89. (PMID: 12952885) Nucleic Acids Res. 2014 Jan;42(Database issue):D922-5. (PMID: 24194607) Mol Biol Evol. 2019 Oct 1;36(10):2157-2164. (PMID: 31241141) Nat Methods. 2016 May;13(5):425-30. (PMID: 27043882) PLoS One. 2012;7(10):e48295. (PMID: 23144748) Genome Res. 2009 Feb;19(2):327-35. (PMID: 19029536) Mol Biol Evol. 2016 Jun;33(6):1635-8. (PMID: 26921390) Genome Biol. 2009;10(9):403. (PMID: 19785718) Bioinformatics. 2020 Feb 15;36(4):1265-1266. (PMID: 31560365) Brief Bioinform. 2011 Sep;12(5):485-8. (PMID: 21666252) Nature. 2015 Mar 12;519(7542):219-22. (PMID: 25487147) Nucleic Acids Res. 2011 Jan;39(Database issue):D556-60. (PMID: 21075798) BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S3. (PMID: 19534752) Genome Biol. 2008 Oct 30;9(10):235. (PMID: 18983710) Bioinformatics. 2012 Mar 15;28(6):900-4. (PMID: 22332236) Nucleic Acids Res. 2016 Jan 4;44(D1):D286-93. (PMID: 26582926) |
| تواريخ الأحداث: | Date Created: 20200429 Date Completed: 20201125 Latest Revision: 20201125 |
| رمز التحديث: | 20221213 |
| مُعرف محوري في PubMed: | PMC7319458 |
| DOI: | 10.1093/nar/gkaa282 |
| PMID: | 32343307 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1362-4962 |
|---|---|
| DOI: | 10.1093/nar/gkaa282 |