The chordate proteome history database
| العنوان: | The chordate proteome history database |
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| المؤلفون: | Olivier Poch, Pierre Pontarotti, Anthony Levasseur, Philippe Gouret, Jacques Dainat, Julien Paganini, Julie D. Thompson |
| المساهمون: | Levasseur, Anthony, Laboratoire d'Analyse, Topologie, Probabilités (LATP), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), ANR EvolHHuPro: ANR-07-BLAN-0054-01 |
| المصدر: | Evolutionary Bioinformatics Evolutionary Bioinformatics Online (8), 437-447. (2012) Evolutionary Bioinformatics, Libertas Academica (New Zealand), 2012, 8, pp.437-47. ⟨10.4137/EBO.S9186⟩ Evolutionary Bioinformatics, Vol 2012, Iss 8, Pp 437-447 (2012) Evolutionary Bioinformatics, Vol 8 (2012) Evolutionary Bioinformatics, 2012, 8, pp.437-47. ⟨10.4137/EBO.S9186⟩ |
| سنة النشر: | 2012 |
| مصطلحات موضوعية: | phylogénétique, alignement de séquences, Genome evolution, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Architecture domain, taille famille, Lineage (evolution), lcsh:Evolution, Genomics, Biology, gène paralogue, genome evolution, computer.software_genre, analyse phylogénétique, gain génétique, 03 medical and health sciences, duplication de gènes, Phylogenetics, Biologie animale, Genetics, lcsh:QH359-425, chordata, base de données protéomique, gène orthologue, protéome, Ecology, Evolution, Behavior and Systematics, protein architecture, 030304 developmental biology, Original Research, Animal biology, 0303 health sciences, Phylogenetic tree, Database, family size, functional inference, ortholog groups, phylogenetic reconstruction, séquence génomique, 030302 biochemistry & molecular biology, Phylogenetic network, réarrangement génétique, Computer Science Applications, protéine, Proteome, évolution du génome, arbre phylogénétique, computer |
| الوصف: | International audience; The chordate proteome history database (http://ioda.univ-provence.frTest) comprises some 20,000 evolutionary analyses of proteins from chordate species. Our main objective was to characterize and study the evolutionary histories of the chordate proteome, and in particular to detect genomic events and automatic functional searches. Firstly, phylogenetic analyses based on high quality multiple sequence alignments and a robust phylogenetic pipeline were performed for the whole protein and for each individual domain. Novel approaches were developed to identify orthologs/paralogs, and predict gene duplication/gain/loss events and the occurrence of new protein architectures (domain gains, losses and shuffling). These important genetic events were localized on the phylogenetic trees and on the genomic sequence. Secondly, the phylogenetic trees were enhanced by the creation of phylogroups, whereby groups of orthologous sequences created using OrthoMCL were corrected based on the phylogenetic trees; gene family size and gene gain/loss in a given lineage could be deduced from the phylogroups. For each ortholog group obtained from the phylogenetic or the phylogroup analysis, functional information and expression data can be retrieved. Database searches can be performed easily using biological objects: protein identifier, keyword or domain, but can also be based on events, eg, domain exchange events can be retrieved. To our knowledge, this is the first database that links group clustering, phylogeny and automatic functional searches along with the detection of important events occurring during genome evolution, such as the appearance of a new domain architecture. |
| وصف الملف: | application/pdf |
| تدمد: | 1176-9343 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ffc387db01f5a859cbe5785a3bc1c0e4Test https://pubmed.ncbi.nlm.nih.gov/22904610Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....ffc387db01f5a859cbe5785a3bc1c0e4 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 11769343 |
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