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Comparative genomics approach to detecting split-coding regions in a low-coverage genome : lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes)

Comparative genomics approach to detecting split-coding regions in a low-coverage genome : lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes)

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DESSIMOZ, Christophe, Stefan ZOLLER, Tereza MANOUSAKI, Huan QIU, Axel MEYER, Shigehiro KURAKU, 2011. Comparative genomics approach to detecting split-coding regions in a low-coverage genome : lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes). In: Briefings in Bioinformatics. 12(5), pp. 474-484. ISSN 1467-5463. eISSN 1477-4054

@article{Dessimoz2011-09Compa-19455, title={Comparative genomics approach to detecting split-coding regions in a low-coverage genome : lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes)}, year={2011}, doi={10.1093/bib/bbr038}, number={5}, volume={12}, issn={1467-5463}, journal={Briefings in Bioinformatics}, pages={474--484}, author={Dessimoz, Christophe and Zoller, Stefan and Manousaki, Tereza and Qiu, Huan and Meyer, Axel and Kuraku, Shigehiro} }

<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bibo="http://purl.org/ontology/bibo/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > <rdf:Description rdf:about="https://kops.uni-konstanz.de/rdf/resource/123456789/19455"> <dc:contributor>Dessimoz, Christophe</dc:contributor> <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2012-06-13T09:42:33Z</dc:date> <dc:creator>Qiu, Huan</dc:creator> <dc:language>eng</dc:language> <bibo:uri rdf:resource="http://kops.uni-konstanz.de/handle/123456789/19455"/> <dc:rights>deposit-license</dc:rights> <dc:contributor>Zoller, Stefan</dc:contributor> <dc:contributor>Qiu, Huan</dc:contributor> <dcterms:rights rdf:resource="http://nbn-resolving.org/urn:nbn:de:bsz:352-20140905103605204-4002607-1"/> <dcterms:title>Comparative genomics approach to detecting split-coding regions in a low-coverage genome : lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes)</dcterms:title> <dc:contributor>Kuraku, Shigehiro</dc:contributor> <dc:contributor>Manousaki, Tereza</dc:contributor> <dc:creator>Zoller, Stefan</dc:creator> <dc:contributor>Meyer, Axel</dc:contributor> <dcterms:abstract xml:lang="eng">Recent development of deep sequencing technologies has facilitated de novo genome sequencing projects, now conducted even by individual laboratories. However, this will yield more and more genome sequences that are not well assembled, and will hinder thorough annotation when no closely related reference genome is available. One of the challenging issues is the identification of protein-coding sequences split into multiple unassembled genomic segments, which can confound orthology assignment and various laboratory experiments requiring the identification of individual genes. In this study, using the genome of a cartilaginous fish, Callorhinchus milii, as test case, we performed gene prediction using a model specifically trained for this genome. We implemented an algorithm, designated ESPRIT, to identify possible linkages between multiple protein-coding portions derived from a single genomic locus split into multiple unassembled genomic segments. We developed a validation framework based on an artificially fragmented human genome, improvements between early and recent mouse genome assemblies, comparison with experimentally validated sequences from GenBank, and phylogenetic analyses. Our strategy provided insights into practical solutions for efficient annotation of only partially sequenced (low-coverage) genomes. To our knowledge, our study is the first formulation of a method to link unassembled genomic segments based on proteomes of relatively distantly related species as references.</dcterms:abstract> <dcterms:bibliographicCitation>Briefings in Bioinformatics ; 12 (2011), 5. - S. 474-484</dcterms:bibliographicCitation> <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2012-06-13T09:42:33Z</dcterms:available> <dcterms:issued>2011-09</dcterms:issued> <dc:creator>Meyer, Axel</dc:creator> <dc:creator>Kuraku, Shigehiro</dc:creator> <dc:creator>Manousaki, Tereza</dc:creator> <dc:creator>Dessimoz, Christophe</dc:creator> </rdf:Description> </rdf:RDF>

Dateiabrufe seit 01.10.2014 (Informationen über die Zugriffsstatistik)

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