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Genome-wide computational prediction of tandem gene arrays: application in yeasts.

hal.structure.identifierGénétique moléculaire, génomique, microbiologie [GMGM]
dc.contributor.authorDESPONS, Laurence
hal.structure.identifierUniversité Catholique de Louvain = Catholic University of Louvain [UCL]
dc.contributor.authorBARET, Philippe
hal.structure.identifierIntégration et Analyse Génomique (Plate-Forme 4) [PF4]
dc.contributor.authorFRANGEUL, Lionel
hal.structure.identifierGénétique moléculaire, génomique, microbiologie [GMGM]
dc.contributor.authorLOUIS, Véronique
hal.structure.identifierModels and Algorithms for the Genome [ MAGNOME]
dc.contributor.authorDURRENS, Pascal
hal.structure.identifierGénétique moléculaire, génomique, microbiologie [GMGM]
dc.contributor.authorSOUCIET, Jean-Luc
dc.date.accessioned2024-04-15T09:45:47Z
dc.date.available2024-04-15T09:45:47Z
dc.date.issued2010
dc.identifier.issn1471-2164
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/197950
dc.description.abstractEnBACKGROUND: This paper describes an efficient in silico method for detecting tandem gene arrays (TGAs) in fully sequenced and compact genomes such as those of prokaryotes or unicellular eukaryotes. The originality of this method lies in the search of protein sequence similarities in the vicinity of each coding sequence, which allows the prediction of tandem duplicated gene copies independently of their functionality. RESULTS: Applied to nine hemiascomycete yeast genomes, this method predicts that 2% of the genes are involved in TGAs and gene relics are present in 11% of TGAs. The frequency of TGAs with degenerated gene copies means that a significant fraction of tandem duplicated genes follows the birth-and-death model of evolution. A comparison of sequence identity distributions between sets of homologous gene pairs shows that the different copies of tandem arrayed paralogs are less divergent than copies of dispersed paralogs in yeast genomes. It suggests that paralogs included in tandem structures are more recent or more subject to the gene conversion mechanism than other paralogs. CONCLUSION: The method reported here is a useful computational tool to provide a database of TGAs composed of functional or nonfunctional gene copies. Such a database has obvious applications in the fields of structural and comparative genomics. Notably, a detailed study of the TGA catalog will make it possible to tackle the fundamental questions of the origin and evolution of tandem gene clusters.
dc.language.isoen
dc.publisherBioMed Central
dc.subject.meshAlgorithms
dc.subject.meshComputational Biology
dc.subject.meshYeasts
dc.subject.meshDatabases, Genetic
dc.subject.meshEvolution, Molecular
dc.subject.meshGenome, Fungal
dc.subject.meshGenomics
dc.subject.meshMinisatellite Repeats
dc.subject.meshOligonucleotide Array Sequence Analysis
dc.subject.meshPhylogeny
dc.subject.meshSequence Analysis, DNA
dc.title.enGenome-wide computational prediction of tandem gene arrays: application in yeasts.
dc.typeArticle de revue
dc.identifier.doi10.1186/1471-2164-11-56
dc.subject.halSciences du Vivant [q-bio]/Biochimie, Biologie Moléculaire/Génomique, Transcriptomique et Protéomique [q-bio.GN]
bordeaux.journalBMC Genomics
bordeaux.page56
bordeaux.volume11
bordeaux.hal.laboratoriesLaboratoire Bordelais de Recherche en Informatique (LaBRI) - UMR 5800*
bordeaux.issue1
bordeaux.institutionUniversité de Bordeaux
bordeaux.institutionBordeaux INP
bordeaux.institutionCNRS
bordeaux.peerReviewedoui
hal.identifierpasteur-00670632
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//pasteur-00670632v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=BMC%20Genomics&rft.date=2010&rft.volume=11&rft.issue=1&rft.spage=56&rft.epage=56&rft.eissn=1471-2164&rft.issn=1471-2164&rft.au=DESPONS,%20Laurence&BARET,%20Philippe&FRANGEUL,%20Lionel&LOUIS,%20V%C3%A9ronique&DURRENS,%20Pascal&rft.genre=article


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