{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,4,5]],"date-time":"2022-04-05T04:53:42Z","timestamp":1649134422953},"reference-count":24,"publisher":"Springer Science and Business Media LLC","issue":"S7","license":[{"start":{"date-parts":[[2010,10,1]],"date-time":"2010-10-01T00:00:00Z","timestamp":1285891200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2010,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Orthologs are genes derived from the same ancestor gene loci after speciation events. Orthologous proteins usually have similar sequences and perform comparable biological functions. Therefore, ortholog identification is useful in annotations of newly sequenced genomes. With rapidly increasing number of sequenced genomes, constructing or updating ortholog relationship between all genomes requires lots of effort and computation time. In addition, elucidating ortholog relationships between distantly related genomes is challenging because of the lower sequence similarity. Therefore, an efficient ortholog detection method that can deal with large number of distantly related genomes is desired.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>An efficient ortholog detection pipeline DODO (DOmain based Detection of Orthologs) is created on the basis of domain architectures in this study. Supported by domain composition, which usually directly related with protein function, DODO could facilitate orthologs detection across distantly related genomes. DODO works in two main steps. Starting from domain information, it first assigns protein groups according to their domain architectures and further identifies orthologs within those groups with much reduced complexity. Here DODO is shown to detect orthologs between two genomes in considerably shorter period of time than traditional methods of reciprocal best hits and it is more significant when analyzed a large number of genomes. The output results of DODO are highly comparable with other known ortholog databases.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>DODO provides a new efficient pipeline for detection of orthologs in a large number of genomes. In addition, a database established with DODO is also easier to maintain and could be updated relatively effortlessly. The pipeline of DODO could be downloaded from <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/140.109.42.19:16080\/dodo_web\/home.htm\" ext-link-type=\"uri\">http:\/\/140.109.42.19:16080\/dodo_web\/home.htm<\/jats:ext-link>\n            <\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-11-s7-s6","type":"journal-article","created":{"date-parts":[[2019,12,11]],"date-time":"2019-12-11T01:59:03Z","timestamp":1576029543000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["DODO: an efficient orthologous genes assignment tool based on domain architectures. Domain based ortholog detection"],"prefix":"10.1186","volume":"11","author":[{"given":"Ting-wen","family":"Chen","sequence":"first","affiliation":[]},{"given":"Timothy H","family":"Wu","sequence":"additional","affiliation":[]},{"given":"Wailap V","family":"Ng","sequence":"additional","affiliation":[]},{"given":"Wen-chang","family":"Lin","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2010,10,15]]},"reference":[{"issue":"2","key":"4244_CR1","doi-asserted-by":"publisher","first-page":"99","DOI":"10.2307\/2412448","volume":"19","author":"WM Fitch","year":"1970","unstructured":"Fitch WM: Distinguishing homologous from analogous proteins. Syst Zool 1970, 19(2):99\u201313. 10.2307\/2412448","journal-title":"Syst Zool"},{"issue":"5","key":"4244_CR2","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1016\/S0168-9525(00)02005-9","volume":"16","author":"WM Fitch","year":"2000","unstructured":"Fitch WM: Homology a personal view on some of the problems. Trends Genet 2000, 16(5):227\u2013231. 10.1016\/S0168-9525(00)02005-9","journal-title":"Trends Genet"},{"issue":"5","key":"4244_CR3","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1038\/nrg1603","volume":"6","author":"F Delsuc","year":"2005","unstructured":"Delsuc F, Brinkmann H, Philippe H: Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 2005, 6(5):361\u2013375. 10.1038\/nrg1603","journal-title":"Nat Rev Genet"},{"issue":"8","key":"4244_CR4","doi-asserted-by":"publisher","first-page":"4285","DOI":"10.1073\/pnas.96.8.4285","volume":"96","author":"M Pellegrini","year":"1999","unstructured":"Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO: Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci USA 1999, 96(8):4285\u20134288. 10.1073\/pnas.96.8.4285","journal-title":"Proc Natl Acad Sci USA"},{"issue":"11","key":"4244_CR5","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1016\/j.tig.2008.08.009","volume":"24","author":"A Kuzniar","year":"2008","unstructured":"Kuzniar A, van Ham RC, Pongor S, Leunissen JA: The quest for orthologs: finding the corresponding gene across genomes. Trends Genet 2008, 24(11):539\u2013551. 10.1016\/j.tig.2008.08.009","journal-title":"Trends Genet"},{"key":"4244_CR6","volume-title":"Nucleic Acids Res","author":"EV Kriventseva","year":"2008","unstructured":"Kriventseva EV, Rahman N, Espinosa O, Zdobnov EM: OrthoDB: the hierarchical catalog of eukaryotic orthologs. Nucleic Acids Res 2008, (36 Database):D271\u2013275."},{"key":"4244_CR7","volume-title":"Nucleic Acids Res","author":"G Ostlund","year":"2010","unstructured":"Ostlund G, Schmitt T, Forslund K, Kostler T, Messina DN, Roopra S, Frings O, Sonnhammer EL: InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res 2010, (38 Database):D196\u2013203. 10.1093\/nar\/gkp931"},{"issue":"1","key":"4244_CR8","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1093\/nar\/28.1.33","volume":"28","author":"RL Tatusov","year":"2000","unstructured":"Tatusov RL, Galperin MY, Natale DA, Koonin EV: The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000, 28(1):33\u201336. 10.1093\/nar\/28.1.33","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"4244_CR9","doi-asserted-by":"publisher","first-page":"779","DOI":"10.1093\/bioinformatics\/btl009","volume":"22","author":"R Jothi","year":"2006","unstructured":"Jothi R, Zotenko E, Tasneem A, Przytycka TM: COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations. Bioinformatics 2006, 22(7):779\u2013788. 10.1093\/bioinformatics\/btl009","journal-title":"Bioinformatics"},{"issue":"10","key":"4244_CR10","doi-asserted-by":"publisher","first-page":"2353","DOI":"10.1101\/gr1305203","volume":"13","author":"CE Storm","year":"2003","unstructured":"Storm CE, Sonnhammer EL: Comprehensive analysis of orthologous protein domains using the HOPS database. Genome Res 2003, 13(10):2353\u20132362. 10.1101\/gr1305203","journal-title":"Genome Res"},{"key":"4244_CR11","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1186\/1471-2105-8-83","volume":"8","author":"RT van der Heijden","year":"2007","unstructured":"van der Heijden RT, Snel B, van Noort V, Huynen MA: Orthology prediction at scalable resolution by phylogenetic tree analysis. BMC Bioinformatics 2007, 8: 83. 10.1186\/1471-2105-8-83","journal-title":"BMC Bioinformatics"},{"key":"4244_CR12","volume-title":"Nucleic Acids Res","author":"TJ Hubbard","year":"2007","unstructured":"Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, et al.: Ensembl 2007. Nucleic Acids Res 2007, (35 Database):D610\u2013617. 10.1093\/nar\/gkl996"},{"issue":"Database issue","key":"4244_CR13","doi-asserted-by":"publisher","first-page":"D5","DOI":"10.1093\/nar\/gkn741","volume":"37","author":"EW Sayers","year":"2009","unstructured":"Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, et al.: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2009, 37(Database issue):D5\u201315. 10.1093\/nar\/gkn741","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"4244_CR14","doi-asserted-by":"publisher","first-page":"1160","DOI":"10.1089\/cmb.2007.0048","volume":"14","author":"Z Fu","year":"2007","unstructured":"Fu Z, Chen X, Vacic V, Nan P, Zhong Y, Jiang T: MSOAR: a high-throughput ortholog assignment system based on genome rearrangement. J Comput Biol 2007, 14(9):1160\u20131175. 10.1089\/cmb.2007.0048","journal-title":"J Comput Biol"},{"issue":"3","key":"4244_CR15","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1142\/S0219720008003540","volume":"6","author":"Z Fu","year":"2008","unstructured":"Fu Z, Jiang T: Clustering of main orthologs for multiple genomes. J Bioinform Comput Biol 2008, 6(3):573\u2013584. 10.1142\/S0219720008003540","journal-title":"J Bioinform Comput Biol"},{"key":"4244_CR16","volume-title":"Nucleic Acids Res","author":"RD Finn","year":"2006","unstructured":"Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, et al.: Pfam: clans, web tools and services. Nucleic Acids Res 2006, (34 Database):D247\u2013251. 10.1093\/nar\/gkj149"},{"issue":"2","key":"4244_CR17","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1016\/j.sbi.2004.03.011","volume":"14","author":"C Vogel","year":"2004","unstructured":"Vogel C, Bashton M, Kerrison ND, Chothia C, Teichmann SA: Structure, function and evolution of multidomain proteins. Current opinion in structural biology 2004, 14(2):208\u2013216. 10.1016\/j.sbi.2004.03.011","journal-title":"Current opinion in structural biology"},{"key":"4244_CR18","volume-title":"Nucleic Acids Res","author":"RD Finn","year":"2008","unstructured":"Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, et al.: The Pfam protein families database. Nucleic Acids Res 2008, (36 Database):D281\u2013288."},{"issue":"4","key":"4244_CR19","doi-asserted-by":"publisher","first-page":"927","DOI":"10.1006\/jmbi.2001.5288","volume":"315","author":"M Bashton","year":"2002","unstructured":"Bashton M, Chothia C: The geometry of domain combination in proteins. Journal of molecular biology 2002, 315(4):927\u2013939. 10.1006\/jmbi.2001.5288","journal-title":"Journal of molecular biology"},{"issue":"5","key":"4244_CR20","doi-asserted-by":"publisher","first-page":"1041","DOI":"10.1006\/jmbi.2000.5197","volume":"314","author":"M Remm","year":"2001","unstructured":"Remm M, Storm CE, Sonnhammer EL: Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. Journal of molecular biology 2001, 314(5):1041\u20131052. 10.1006\/jmbi.2000.5197","journal-title":"Journal of molecular biology"},{"issue":"1","key":"4244_CR21","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25(1):25\u201329. 10.1038\/75556","journal-title":"Nat Genet"},{"issue":"27","key":"4244_CR22","doi-asserted-by":"publisher","first-page":"11079","DOI":"10.1073\/pnas.0905029106","volume":"106","author":"M Levitt","year":"2009","unstructured":"Levitt M: Nature of the protein universe. Proc Natl Acad Sci USA 2009, 106(27):11079\u201311084. 10.1073\/pnas.0905029106","journal-title":"Proc Natl Acad Sci USA"},{"issue":"1","key":"4244_CR23","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1093\/bioinformatics\/18.1.92","volume":"18","author":"CE Storm","year":"2002","unstructured":"Storm CE, Sonnhammer EL: Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics 2002, 18(1):92\u201399. 10.1093\/bioinformatics\/18.1.92","journal-title":"Bioinformatics"},{"key":"4244_CR24","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1186\/1471-2105-3-14","volume":"3","author":"CM Zmasek","year":"2002","unstructured":"Zmasek CM, Eddy SR: RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics 2002, 3: 14. 10.1186\/1471-2105-3-14","journal-title":"BMC Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-S7-S6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-11-S7-S6\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-S7-S6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T04:38:34Z","timestamp":1630471114000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-11-S7-S6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,10]]},"references-count":24,"journal-issue":{"issue":"S7","published-print":{"date-parts":[[2010,10]]}},"alternative-id":["4244"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-11-s7-s6","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,10]]},"assertion":[{"value":"15 October 2010","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S6"}}