{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T11:38:02Z","timestamp":1770982682511,"version":"3.50.1"},"reference-count":78,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2008,5,16]],"date-time":"2008-05-16T00:00:00Z","timestamp":1210896000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1000063","type":"journal-article","created":{"date-parts":[[2008,5,16]],"date-time":"2008-05-16T04:01:39Z","timestamp":1210910499000},"page":"e1000063","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":60,"title":["Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins"],"prefix":"10.1371","volume":"4","author":[{"given":"Nan","family":"Song","sequence":"first","affiliation":[]},{"given":"Jacob M.","family":"Joseph","sequence":"additional","affiliation":[]},{"given":"George B.","family":"Davis","sequence":"additional","affiliation":[]},{"given":"Dannie","family":"Durand","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2008,5,16]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/S1476-9271(02)00098-1","article-title":"Protein family classification and functional annotation.","volume":"27","author":"C Wu","year":"2003","journal-title":"Comput Biol Chem"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"4285","DOI":"10.1073\/pnas.96.8.4285","article-title":"Assigning protein functions by comparative genome analysis: protein phylogenetic profiles.","volume":"96","author":"M Pellegrini","year":"1999","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1126\/science.285.5428.751","article-title":"Detecting protein function and protein\u2013protein interactions from genome sequences.","volume":"285","author":"E Marcotte","year":"1999","journal-title":"Science"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1038\/47056","article-title":"Protein interaction maps for complete genomes based on gene fusion events.","volume":"402","author":"A Enright","year":"1999","journal-title":"Nature"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1371\/journal.pcbi.0020077","article-title":"Functional classification using phylogenomic inference.","volume":"2","author":"D Brown","year":"2006","journal-title":"PLoS Comput Biol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"2896","DOI":"10.1073\/pnas.96.6.2896","article-title":"The use of gene clusters to infer functional coupling.","volume":"96","author":"R Overbeek","year":"1999","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1016\/S0968-0004(98)01274-2","article-title":"Conservation of gene order: a fingerprint of proteins that physically interact.","volume":"23","author":"T Dandekar","year":"1998","journal-title":"Trends Biochem Sci"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1016\/S0168-9525(98)01607-2","article-title":"Counting on comparative maps.","volume":"14","author":"J Nadeau","year":"1998","journal-title":"Trends Genet"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1016\/S0168-9525(97)01297-3","article-title":"Comparative genomics: lessons from cats.","volume":"10","author":"S O'Brien","year":"1997","journal-title":"Trends Genet"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1016\/j.tig.2006.01.002","article-title":"Diagnosing duplications: can it be done?","volume":"22","author":"D Durand","year":"2006","journal-title":"Trends Genet"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1038\/nrg1449","article-title":"Computational approaches to unveiling ancient genome duplications.","volume":"5","author":"Y Van de Peer","year":"2004","journal-title":"Nat Rev Genet"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1093\/bfgp\/3.4.332","article-title":"The identification and functional characterisation of conserved regulatory elements in developmental genes.","volume":"3","author":"T Dickmeis","year":"2005","journal-title":"Brief Funct Genomic Proteomic"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"2147","DOI":"10.1093\/nar\/gkh510","article-title":"Operon prediction by comparative genomics: an application to the <italic>Synechococcus<\/italic> sp. WH8102 genome.","volume":"32","author":"X Chen","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"880","DOI":"10.1093\/nar\/gki232","article-title":"A novel method for accurate operon predictions in all sequenced prokaryotes.","volume":"33","author":"M Price","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"880","DOI":"10.1093\/bioinformatics\/bti123","article-title":"Operon prediction without a training set.","volume":"21","author":"B Westover","year":"2005","journal-title":"Bioinformatics"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/j.jchromb.2004.11.010","article-title":"Survey of current protein family databases and their application in comparative, structural and functional genomics.","volume":"815","author":"O Redfern","year":"2005","journal-title":"J Chromatogr B Analyt Technol Biomed Life Sci"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"5064","DOI":"10.1111\/j.1742-4658.2005.04917.x","article-title":"Modules, multidomain proteins and organismic complexity.","volume":"272","author":"H Tordai","year":"2005","journal-title":"FEBS J"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"99","DOI":"10.2307\/2412448","article-title":"Distinguishing homologous from analogous proteins.","volume":"19","author":"W Fitch","year":"1970","journal-title":"Syst Zool"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"5548","DOI":"10.1038\/sj.onc.1203957","article-title":"The protein tyrosine kinase family of the human genome.","volume":"19","author":"D Robinson","year":"2000","journal-title":"Oncogene"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1186\/gb-2003-4-5-111","article-title":"Genomic analysis of the eukaryotic protein kinase superfamily: a perspective.","volume":"4","author":"S Hanks","year":"2003","journal-title":"Genome Biol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1016\/S0022-2836(02)00538-7","article-title":"Sequence and structure classification of kinases.","volume":"320","author":"S Cheek","year":"2002","journal-title":"J Mol Biol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"e49","DOI":"10.1371\/journal.pcbi.0010049","article-title":"Structural evolution of the protein kinase-like superfamily.","volume":"1","author":"ED Scheeff","year":"2005","journal-title":"PLoS Comput Biol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1089\/cmb.2007.A009","article-title":"Domain architecture comparison for multidomain homology identification.","volume":"14","author":"N Song","year":"2007","journal-title":"J Comput Biol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"911","DOI":"10.1016\/j.jmb.2005.08.067","article-title":"Domain rearrangements in protein evolution.","volume":"353","author":"A Bjorklund","year":"2005","journal-title":"J Mol Biol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"1619","DOI":"10.1101\/gr.278202","article-title":"CDART: protein homology by domain architecture.","volume":"12","author":"L Geer","year":"2002","journal-title":"Genome Res"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"2081","DOI":"10.1093\/bioinformatics\/btl366","article-title":"An initial strategy for comparing proteins at the domain architecture level.","volume":"22","author":"K Lin","year":"2006","journal-title":"Bioinformatics"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"5849","DOI":"10.1073\/pnas.95.11.5849","article-title":"Measuring genome evolution.","volume":"95","author":"M Huynen","year":"1998","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref28","first-page":"11","article-title":"Gene order and phylogenetic reconstruction: application to gamma-Proteobacteria.","author":"G Blin","year":"2005"},{"key":"ref29","first-page":"578","article-title":"A parsimony approach to genome-wide orthology assignment.","author":"Z Fu","year":"2006"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1109\/TCBB.2005.48","article-title":"Assignment of orthologous genes via genome rearrangement.","volume":"2","author":"X Chen","year":"2005","journal-title":"IEEE\/ACM Transactions on Computational Biology and Bioinformatics"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1046","DOI":"10.1038\/35082561","article-title":"Protein dispensability and rate of evolution.","volume":"411","author":"A Hirsh","year":"2001","journal-title":"Nature"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1038\/ng884","article-title":"Extensive genomic duplication during early chordate evolution.","volume":"31","author":"A McLysaght","year":"2002","journal-title":"Nat Genet"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1101\/gr.751803","article-title":"A recent polyploidy superimposed on older large-scale duplications in the <italic>Arabidopsis<\/italic> genome.","volume":"13","author":"G Blanc","year":"2003","journal-title":"Genome Res"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"2204","DOI":"10.1126\/science.287.5461.2204","article-title":"Comparative genomics of the eukaryotes.","volume":"287","author":"G Rubin","year":"2000","journal-title":"Science"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1038\/35057039","article-title":"Evolutionary analyses of the human genome.","volume":"409","author":"W Li","year":"2001","journal-title":"Nature"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"2157","DOI":"10.1126\/science.1080049","article-title":"The draft genome of <italic>Ciona intestinalis<\/italic>: Insights into chordate and vertebrate origins.","volume":"298","author":"P Dehal","year":"2002","journal-title":"Science"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1006\/jmbi.2000.5197","article-title":"Automatic clustering of orthologs and in-paralogs from pairwise species comparisons.","volume":"314","author":"M Remm","year":"2001","journal-title":"J Mol Biol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1016\/S0022-2836(05)80134-2","article-title":"SCOP: a structural classification of proteins database for the investigation of sequences and structures.","volume":"247","author":"A Murzin","year":"1995","journal-title":"J Mol Biol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1093\/nar\/gkg062","article-title":"The CATH database: an extended protein family resource for structural and functional genomics.","volume":"31","author":"F Pearl","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1186\/1471-2105-4-41","article-title":"The COG database: an updated version includes eukaryotes.","volume":"4","author":"R Tatusov","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"D247","DOI":"10.1093\/nar\/gkj149","article-title":"Pfam: clans, web tools and services.","volume":"34","author":"RD Finn","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/S0168-9525(00)02005-9","article-title":"Homology: a personal view on some of the problems.","volume":"16","author":"W Fitch","year":"2000","journal-title":"Trends Genet"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1126\/science.4001923","article-title":"Genes-in-pieces revisited.","volume":"228","author":"W Gilbert","year":"1985","journal-title":"Science"},{"key":"ref44","first-page":"339","article-title":"Homology in molecular biology.","author":"D Hillis","year":"1994"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1016\/S1367-5931(02)00003-0","article-title":"Domains, motifs and clusters in the protein universe.","volume":"7","author":"J Liu","year":"2003","journal-title":"Curr Opin Chem Biol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"1018","DOI":"10.1002\/bies.1147","article-title":"Divergence pattern of animal gene families and relationship with the Cambrian explosion.","volume":"23","author":"T Miyata","year":"2001","journal-title":"Bioessays"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"RE9","DOI":"10.1126\/stke.2003.187.re9","article-title":"Signaling receptome: a genomic and evolutionary perspective of plasma membrane receptors involved in signal transduction.","volume":"2003","author":"I Ben-Shlomo","year":"2003","journal-title":"Sci STKE"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/47048","article-title":"A combined algorithm for genome-wide prediction of protein function.","volume":"402","author":"E Marcotte","year":"1999","journal-title":"Nature"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/0014-5793(87)80002-9","article-title":"Intron-dependent evolution: preferred types of exons and introns.","volume":"214","author":"L Patthy","year":"1987","journal-title":"FEBS Lett"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1038\/nature02777","article-title":"Cyclophilin A retrotransposition into TRIM5 explains owl monkey resistance to HIV-1.","volume":"430","author":"D Sayah","year":"2004","journal-title":"Nature"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1038\/nrg1204","article-title":"The origin of new genes: glimpses from the young and old.","volume":"4","author":"M Long","year":"2003","journal-title":"Nat Rev Genet"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"3220","DOI":"10.1073\/pnas.0511307103","article-title":"Evolutionary fate of retroposed gene copies in the human genome.","volume":"103","author":"N Vinckenbosch","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1534\/genetics.104.037283","article-title":"Origin and evolution of a chimeric fusion gene in <italic>Drosophila subobscura<\/italic>, <italic>D. madeirensis<\/italic> and <italic>D. guanche<\/italic>.","volume":"170","author":"C Jones","year":"2005","journal-title":"Genetics"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1186\/1471-2148-7-187","article-title":"Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates.","volume":"7","author":"I Fumasoni","year":"2007","journal-title":"BMC Evol Biol"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/j.jmb.2006.11.017","article-title":"Modeling the evolution of protein domain architectures using maximum parsimony.","volume":"366","author":"J Fong","year":"2007","journal-title":"J Mol Biol"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"2037","DOI":"10.1111\/j.1742-4658.2006.05220.x","article-title":"Domain deletions and substitutions in the modular protein evolution.","volume":"273","author":"J Weiner","year":"2006","journal-title":"FEBS J"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/j.tig.2004.11.007","article-title":"Relative rates of gene fusion and fission in mutli-domain proteins.","volume":"21","author":"S Kummerfeld","year":"2005","journal-title":"Trends Genet"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.","volume":"25","author":"S Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.","volume":"25","author":"M Ashburner","year":"2000","journal-title":"Nat Genet"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"508","DOI":"10.1038\/nrg1113","article-title":"Classification schemes for protein structure and function.","volume":"4","author":"C Ouzounis","year":"2003","journal-title":"Nat Rev Genet"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool.","volume":"215","author":"S Altschul","year":"1990","journal-title":"Journal of Molecular Biology"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"2994","DOI":"10.1093\/nar\/29.14.2994","article-title":"Improving the accuracy of PSI- BLAST protein database searches with composition-based statistics and other refinements.","volume":"29","author":"A Schaffer","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"2637","DOI":"10.1007\/s00018-003-3114-8","article-title":"Automatic prediction of protein function.","volume":"60","author":"B Rost","year":"2003","journal-title":"Cell Mol Life Sci"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"5101","DOI":"10.1111\/j.1742-4658.2005.04945.x","article-title":"Protein database searches using compositionally adjusted substitution matrices.","volume":"272","author":"S Altschul","year":"2005","journal-title":"FEBS J"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"1694","DOI":"10.1093\/oxfordjournals.molbev.a003957","article-title":"Scale free behavior in protein domain networks.","volume":"18","author":"S Wuchty","year":"2001","journal-title":"Mol Biol Evol"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/1471-2148-2-18","article-title":"Birth and death of protein domains: a simple model of evolution explains power law behavior.","volume":"2","author":"G Karev","year":"2002","journal-title":"BMC Evol Biol"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1186\/1471-2148-4-32","article-title":"Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models.","volume":"4","author":"G Karev","year":"2004","journal-title":"BMC Evol Biol"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"988","DOI":"10.1093\/bioinformatics\/17.10.988","article-title":"Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome.","volume":"17","author":"A Rzhetsky","year":"2001","journal-title":"Bioinformatics"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1101\/gr.GR-1619R","article-title":"Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context.","volume":"11","author":"Y Wolf","year":"2001","journal-title":"Genome Res"},{"key":"ref70","doi-asserted-by":"crossref","DOI":"10.1089\/cmb.2006.13.351","article-title":"Graph theoretical insights into evolution of multidomain proteins.","volume":"13","author":"T Przytycka","year":"2006","journal-title":"J Comput Biol"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1089\/cmb.2007.R001","article-title":"Stability of characters and construction of phylogenetic trees.","volume":"14","author":"T Przytycka","year":"2007","journal-title":"J Comput Biol"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"e173","DOI":"10.1371\/journal.pcbi.0020173","article-title":"Protein homology network families reveal step-wise diversification of Type III and Type IV secretion systems.","volume":"2","author":"D Medini","year":"2006","journal-title":"PLoS Comput Biol"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1146\/annurev.genet.35.102401.090145","article-title":"Building a multicellular organism.","volume":"35","author":"D Kaiser","year":"2001","journal-title":"Annu Rev Genet"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"D154","DOI":"10.1093\/nar\/gki070","article-title":"The universal protein resource (UniProt).","volume":"33","author":"A Bairoch","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref75","article-title":"Homology Identification for Multidomain Proteins.","author":"N Song","year":"2007"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"D201","DOI":"10.1093\/nar\/gki106","article-title":"InterPro, progress and status in 2005.","volume":"33","author":"N Mulder","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1016\/S0076-6879(96)66035-2","article-title":"Analysis of compositionally biased regions in sequence databases.","volume":"266","author":"J Wootton","year":"1996","journal-title":"Methods Enzymol"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/S0097-8485(96)80004-0","article-title":"Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching.","volume":"20","author":"M Gribskov","year":"1996","journal-title":"Comput Chem"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000063","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,18]],"date-time":"2023-05-18T11:09:44Z","timestamp":1684408184000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000063"}},"subtitle":[],"editor":[{"given":"Christine","family":"Vogel","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2008,5,16]]},"references-count":78,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2008,5,16]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000063","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,5,16]]}}}