{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T20:16:45Z","timestamp":1780085805230,"version":"3.54.0"},"reference-count":55,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Gene fusion is an important evolutionary process. It can yield valuable information to infer the interactions and functions of proteins. Fused genes have been identified as non-transitive patterns of similarity in triplets of genes. To be computationally tractable, this approach usually imposes an a priori distinction between a dataset in which fused genes are searched for, and a dataset that may have provided genetic material for fusion. This reduces the \u2018genetic space\u2019 in which fusion can be discovered, as only a subset of triplets of genes is investigated. Moreover, this approach may have a high\u2013false-positive rate, and it does not identify gene families descending from a common fusion event.<\/jats:p>\n               <jats:p>Results: We represent similarities between sequences as a network. This leads to an efficient formulation of previous methods of fused gene identification, which we implemented in the Python program FusedTriplets. Furthermore, we propose a new characterization of families of fused genes, as clique minimal separators of the sequence similarity network. This well-studied graph topology provides a robust and fast method of detection, well suited for automatic analyses of big datasets. We implemented this method in the C++ program MosaicFinder, which additionally uses local alignments to discard false-positive candidates and indicates potential fusion points. The grouping into families will help distinguish sequencing or prediction errors from real biological fusions, and it will yield additional insight into the function and history of fused genes.<\/jats:p>\n               <jats:p>Availability: FusedTriplets and MosaicFinder are published under the GPL license and are freely available with their source code at this address: http:\/\/sourceforge.net\/projects\/mosaicfinder.<\/jats:p>\n               <jats:p>Contact: pogorelc@isima.fr<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt049","type":"journal-article","created":{"date-parts":[[2013,1,31]],"date-time":"2013-01-31T04:26:55Z","timestamp":1359606415000},"page":"837-844","source":"Crossref","is-referenced-by-count":28,"title":["MosaicFinder: identification of fused gene families in sequence similarity networks"],"prefix":"10.1093","volume":"29","author":[{"given":"Pierre-Alain","family":"Jachiet","sequence":"first","affiliation":[{"name":"1 UMR CNRS 7138 Syst\u00e9matique, Adaptation, Evolution, Universit\u00e9 Pierre et Marie Curie, 75005 Paris, France and 2LIMOS, Ensemble Scientifique des Cezeaux, 63173 AUBIERE, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Romain","family":"Pogorelcnik","sequence":"additional","affiliation":[{"name":"1 UMR CNRS 7138 Syst\u00e9matique, Adaptation, Evolution, Universit\u00e9 Pierre et Marie Curie, 75005 Paris, France and 2LIMOS, Ensemble Scientifique des Cezeaux, 63173 AUBIERE, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne","family":"Berry","sequence":"additional","affiliation":[{"name":"1 UMR CNRS 7138 Syst\u00e9matique, Adaptation, Evolution, Universit\u00e9 Pierre et Marie Curie, 75005 Paris, France and 2LIMOS, Ensemble Scientifique des Cezeaux, 63173 AUBIERE, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philippe","family":"Lopez","sequence":"additional","affiliation":[{"name":"1 UMR CNRS 7138 Syst\u00e9matique, Adaptation, Evolution, Universit\u00e9 Pierre et Marie Curie, 75005 Paris, France and 2LIMOS, Ensemble Scientifique des Cezeaux, 63173 AUBIERE, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric","family":"Bapteste","sequence":"additional","affiliation":[{"name":"1 UMR CNRS 7138 Syst\u00e9matique, Adaptation, Evolution, Universit\u00e9 Pierre et Marie Curie, 75005 Paris, France and 2LIMOS, Ensemble Scientifique des Cezeaux, 63173 AUBIERE, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,1,30]]},"reference":[{"key":"2023020303310024000_btt049-B1","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1007\/s00239-005-0226-9","article-title":"Mitochondrial genome dynamics in plants and animals: convergent gene fusions of a MutS homologue","volume":"63","author":"Abdelnoor","year":"2006","journal-title":"J. Mol. Evol."},{"key":"2023020303310024000_btt049-B2","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/j.jmb.2004.04.047","article-title":"LGL: creating a map of protein function with an algorithm for visualizing very large biological networks","volume":"340","author":"Adai","year":"2004","journal-title":"J. Mol. Biol."},{"key":"2023020303310024000_btt049-B3","doi-asserted-by":"crossref","first-page":"1313","DOI":"10.1134\/S000629790712005X","article-title":"Do we need many genes for phylogenetic inference?","volume":"72","author":"Aleshin","year":"2007","journal-title":"Biochemistry (Mosc.)"},{"key":"2023020303310024000_btt049-B4","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":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"2023020303310024000_btt049-B5","doi-asserted-by":"crossref","first-page":"e4345","DOI":"10.1371\/journal.pone.0004345","article-title":"Using sequence similarity networks for visualization of relationships across diverse protein superfamilies","volume":"4","author":"Atkinson","year":"2009","journal-title":"PLoS ONE"},{"key":"2023020303310024000_btt049-B6","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1007\/s10539-010-9218-2","article-title":"On the need for integrative phylogenomics, and some steps toward its creation","volume":"25","author":"Bapteste","year":"2010","journal-title":"Biol. Philos."},{"key":"2023020303310024000_btt049-B7","doi-asserted-by":"crossref","first-page":"18266","DOI":"10.1073\/pnas.1206541109","article-title":"Evolutionary analyses of non-genealogical bonds produced by introgressive descent","volume":"109","author":"Bapteste","year":"2012","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020303310024000_btt049-B8","doi-asserted-by":"crossref","first-page":"197","DOI":"10.3390\/a3020197","article-title":"An introduction to clique minimal separator decomposition","volume":"3","author":"Berry","year":"2010","journal-title":"Algorithms"},{"key":"2023020303310024000_btt049-B9","doi-asserted-by":"crossref","first-page":"R74","DOI":"10.1186\/gb-2010-11-7-r74","article-title":"Quantifying the mechanisms of domain gain in animal proteins","volume":"11","author":"Buljan","year":"2010","journal-title":"Genome Biol."},{"key":"2023020303310024000_btt049-B10","doi-asserted-by":"crossref","first-page":"e1000200","DOI":"10.1371\/journal.pcbi.1000200","article-title":"Fusion and fission of genes define a metric between fungal genomes","volume":"4","author":"Durrens","year":"2008","journal-title":"PLoS Comput. Biol."},{"key":"2023020303310024000_btt049-B11","doi-asserted-by":"crossref","first-page":"1337","DOI":"10.1016\/j.jmb.2007.06.022","article-title":"Quantification of the elevated rate of domain rearrangements in metazoa","volume":"372","author":"Ekman","year":"2007","journal-title":"J. Mol. Biol."},{"key":"2023020303310024000_btt049-B12","doi-asserted-by":"crossref","first-page":"10034","DOI":"10.1186\/gb-2001-2-9-research0034","article-title":"Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions","volume":"2","author":"Enright","year":"2001","journal-title":"Genome Biol."},{"key":"2023020303310024000_btt049-B13","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1093\/bioinformatics\/16.5.451","article-title":"GeneRAGE: a robust algorithm for sequence clustering and domain detection","volume":"16","author":"Enright","year":"2000","journal-title":"Bioinformatics"},{"key":"2023020303310024000_btt049-B14","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":"Enright","year":"1999","journal-title":"Nature"},{"key":"2023020303310024000_btt049-B15","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1093\/nar\/30.7.1575","article-title":"An efficient algorithm for large-scale detection of protein families","volume":"30","author":"Enright","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023020303310024000_btt049-B16","doi-asserted-by":"crossref","first-page":"S4","DOI":"10.1186\/1471-2148-7-S2-S4","article-title":"The role of gene fusions in the evolution of metabolic pathways: the histidine biosynthesis case","volume":"7","author":"Fani","year":"2007","journal-title":"BMC Evol. Biol"},{"key":"2023020303310024000_btt049-B55","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1186\/1471-2105-11-86","article-title":"Enrichment of homologs in insignificant BLAST hits by co-complex network alignment","volume":"11","author":"Fokkens","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023020303310024000_btt049-B17","doi-asserted-by":"crossref","first-page":"1109","DOI":"10.1111\/j.1365-2958.2011.07757.x","article-title":"Independent evolutionary origins of functional polyamine biosynthetic enzyme fusions catalysing de novo diamine to triamine formation","volume":"81","author":"Green","year":"2011","journal-title":"Mol. Microbiol."},{"key":"2023020303310024000_btt049-B18","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1073\/pnas.0908978107","article-title":"Network analyses structure genetic diversity in independent genetic worlds","volume":"107","author":"Halary","year":"2009","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020303310024000_btt049-B19","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1038\/nrm2144","article-title":"The folding and evolution of multidomain proteins","volume":"8","author":"Han","year":"2007","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"2023020303310024000_btt049-B20","first-page":"656","article-title":"BLATThe BLAST-like alignment tool","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"2023020303310024000_btt049-B21","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1101\/gr.115782.110","article-title":"RAF gene fusion breakpoints in pediatric brain tumors are characterized by significant enrichment of sequence microhomology","volume":"21","author":"Lawson","year":"2011","journal-title":"Genome Res."},{"key":"2023020303310024000_btt049-B22","doi-asserted-by":"crossref","first-page":"1655","DOI":"10.1101\/gr.165700","article-title":"A new function evolved from gene fusion","volume":"10","author":"Long","year":"2000","journal-title":"Genome Res."},{"key":"2023020303310024000_btt049-B23","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.gene.2007.02.009","article-title":"Occurrence of multiple, independent gene fusion events for the fifth and sixth enzymes of pyrimidine biosynthesis in different eukaryotic groups","volume":"394","author":"Makiuchi","year":"2007","journal-title":"Gene"},{"key":"2023020303310024000_btt049-B24","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1126\/science.285.5428.751","article-title":"Detecting protein function and protein-protein interactions from genome sequences","volume":"285","author":"Marcotte","year":"1999","journal-title":"Science"},{"key":"2023020303310024000_btt049-B25","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1186\/gb-2010-11-7-126","article-title":"How do proteins gain new domains?","volume":"11","author":"Marsh","year":"2010","journal-title":"Genome Biol"},{"key":"2023020303310024000_btt049-B26","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1007\/s00239-009-9258-x","article-title":"Fusion and retrotransposition events in the evolution of the sea anemone Anemonia viridis neurotoxin genes","volume":"69","author":"Moran","year":"2009","journal-title":"J. Mol. Evol."},{"key":"2023020303310024000_btt049-B27","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1093\/molbev\/msl138","article-title":"Rate and polarity of gene fusion and fission in Oryza sativa and Arabidopsis thaliana","volume":"24","author":"Nakamura","year":"2007","journal-title":"Mol. Biol. Evol."},{"key":"2023020303310024000_btt049-B28","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.cancergencyto.2009.02.004","article-title":"Genes that contribute to cancer fusion genes are large and evolutionarily conserved","volume":"191","author":"Narsing","year":"2009","journal-title":"Cancer Genet. Cytogenet"},{"key":"2023020303310024000_btt049-B29","doi-asserted-by":"crossref","first-page":"7279","DOI":"10.1128\/AEM.00203-11","article-title":"Two novel alkane hydroxylase-rubredoxin fusion genes isolated from a dietzia bacterium and the functions of fused rubredoxin domains in long-chain n-alkane degradation","volume":"77","author":"Nie","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"key":"2023020303310024000_btt049-B30","doi-asserted-by":"crossref","first-page":"1469","DOI":"10.1093\/molbev\/msp064","article-title":"Origin and ascendancy of a chimeric fusion gene: the beta\/delta-globin gene of paenungulate mammals","volume":"26","author":"Opazo","year":"2009","journal-title":"Mol. Biol. Evol."},{"key":"2023020303310024000_btt049-B31","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1006\/jmbi.1997.1288","article-title":"Intermediate sequences increase the detection of homology between sequences","volume":"273","author":"Park","year":"1997","journal-title":"J. Mol. Biol."},{"key":"2023020303310024000_btt049-B32","doi-asserted-by":"crossref","first-page":"1418","DOI":"10.1093\/bioinformatics\/btl135","article-title":"Gene fusion\/fission is a major contributor to evolution of multi-domain bacterial proteins","volume":"22","author":"Pasek","year":"2006","journal-title":"Bioinformatics"},{"key":"2023020303310024000_btt049-B33","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1023\/A:1024182432483","article-title":"Modular assembly of genes and the evolution of new functions","volume":"118","author":"Patthy","year":"2003","journal-title":"Genetica"},{"key":"2023020303310024000_btt049-B34","first-page":"235","article-title":"Seq-gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees","volume":"13","author":"Rambaut","year":"1997","journal-title":"Comput. Appl. Biosci."},{"key":"2023020303310024000_btt049-B35","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1093\/bioinformatics\/btl633","article-title":"Enrichment or depletion of a GO category within a class of genes: which test?","volume":"23","author":"Rivals","year":"2007","journal-title":"Bioinformatics"},{"key":"2023020303310024000_btt049-B36","doi-asserted-by":"crossref","first-page":"5405","DOI":"10.1128\/JB.00465-07","article-title":"Bifunctional CTP: inositol-1-phosphate cytidylyltransferase\/CDP-inositol: inositol-1-phosphate transferase, the key enzyme for di-myo-inositol-phosphate synthesis in several (hyper) thermophiles","volume":"189","author":"Rodrigues","year":"2007","journal-title":"J. Bacteriol."},{"key":"2023020303310024000_btt049-B37","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1093\/molbev\/msr184","article-title":"Chimeric genes as a source of rapid evolution in Drosophila melanogaster","volume":"29","author":"Rogers","year":"2012","journal-title":"Mol. Biol. Evol."},{"key":"2023020303310024000_btt049-B38","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1534\/genetics.108.091538","article-title":"Formation and longevity of chimeric and duplicate genes in Drosophila melanogaster","volume":"181","author":"Rogers","year":"2009","journal-title":"Genetics"},{"key":"2023020303310024000_btt049-B39","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1186\/1471-2105-12-279","article-title":"deFuser\/detection of fused genes in eukaryotic genomes using gene deFuser: analysis of the Tetrahymena thermophila genome","volume":"12","author":"Salim","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023020303310024000_btt049-B40","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"2023020303310024000_btt049-B41","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","article-title":"Identification of common molecular subsequences","volume":"147","author":"Smith","year":"1981","journal-title":"J. Mol. Biol."},{"key":"2023020303310024000_btt049-B42","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/S0168-9525(99)01924-1","article-title":"Genome evolution-gene fusion versus gene fission","volume":"16","author":"Snel","year":"2000","journal-title":"Trends Genet."},{"key":"2023020303310024000_btt049-B43","doi-asserted-by":"crossref","first-page":"e1000063","DOI":"10.1371\/journal.pcbi.1000063","article-title":"Sequence similarity network reveals common ancestry of multidomain proteins","volume":"4","author":"Song","year":"2008","journal-title":"PLoS Comput. Biol."},{"key":"2023020303310024000_btt049-B44","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1126\/science.1071196","article-title":"Rooting the eukaryote tree by using a derived gene fusion","volume":"297","author":"Stechmann","year":"2002","journal-title":"Science"},{"key":"2023020303310024000_btt049-B45","doi-asserted-by":"crossref","first-page":"273D","DOI":"10.1093\/nar\/gkh053","article-title":"FusionDB: a database for in-depth analysis of prokaryotic gene fusion events","volume":"32","author":"Suhre","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023020303310024000_btt049-B46","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1126\/science.278.5338.631","article-title":"A genomic perspective on protein families","volume":"278","author":"Tatusov","year":"1997","journal-title":"Science"},{"key":"2023020303310024000_btt049-B47","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":"Tatusov","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"2023020303310024000_btt049-B48","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":"Tordai","year":"2005","journal-title":"FEBS J."},{"key":"2023020303310024000_btt049-B49","doi-asserted-by":"crossref","first-page":"1437","DOI":"10.1093\/molbev\/msl008","article-title":"Lateral gene transfer of a multigene region from cyanobacteria to dinoflagellates resulting in a novel plastid-targeted fusion protein","volume":"23","author":"Waller","year":"2006","journal-title":"Mol. Biol. Evol."},{"key":"2023020303310024000_btt049-B50","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1093\/molbev\/msr222","article-title":"Evolution at the subgene level: domain rearrangements in the Drosophila phylogeny","volume":"29","author":"Wu","year":"2011","journal-title":"Mol. Biol. Evol."},{"key":"2023020303310024000_btt049-B51","doi-asserted-by":"crossref","first-page":"7940","DOI":"10.1073\/pnas.141236298","article-title":"Genes linked by fusion events are generally of the same functional category: a systematic analysis of 30 microbial genomes","volume":"98","author":"Yanai","year":"2001","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020303310024000_btt049-B52","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.gene.2004.04.025","article-title":"Ancestral gene fusion in cellobiose dehydrogenases reflects a specific evolution of GMC oxidoreductases in fungi","volume":"338","author":"Zamocky","year":"2004","journal-title":"Gene"},{"key":"2023020303310024000_btt049-B53","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1111\/j.1574-695X.2010.00769.x","article-title":"ALS51, a newly discovered gene in the Candida albicans ALS family, created by intergenic recombination: analysis of the gene and protein, and implications for evolution of microbial gene families","volume":"61","author":"Zhao","year":"2011","journal-title":"FEMS Immunol. Med. Microbiol"},{"key":"2023020303310024000_btt049-B54","doi-asserted-by":"crossref","first-page":"1446","DOI":"10.1101\/gr.076588.108","article-title":"On the origin of new genes in Drosophila","volume":"18","author":"Zhou","year":"2008","journal-title":"Genome Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/7\/837\/49060883\/bioinformatics_29_7_837.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/7\/837\/49060883\/bioinformatics_29_7_837.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,3]],"date-time":"2023-02-03T03:32:58Z","timestamp":1675395178000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/7\/837\/252807"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,1,30]]},"references-count":55,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2013,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt049","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,4,1]]},"published":{"date-parts":[[2013,1,30]]}}}