Gene finding in the chicken genome
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- dc.contributor.author Eyras Jiménez, Eduardoca
- dc.contributor.author Reymond, Alexandreca
- dc.contributor.author Castelo Valdueza, Robertca
- dc.contributor.author Bye, Jacqueline M.ca
- dc.contributor.author Cámara, Franciscoca
- dc.contributor.author Flicek, Paulca
- dc.contributor.author Huckle, Elizabeth J.ca
- dc.contributor.author Parra Farré, Genísca
- dc.contributor.author Shteynberg, David D.ca
- dc.contributor.author Wyss, Carineca
- dc.contributor.author Rogers, Janeca
- dc.contributor.author Antonarakis, Stylianos E.ca
- dc.contributor.author Birney, Ewanca
- dc.contributor.author Guigó Serra, Rodericca
- dc.contributor.author Brent, Michael R.ca
- dc.date.accessioned 2011-11-28T11:08:15Z
- dc.date.available 2011-11-28T11:08:15Z
- dc.date.issued 2005ca
- dc.description.abstract Background: Despite the continuous production of genome sequence for a number of organisms,/nreliable, comprehensive, and cost effective gene prediction remains problematic. This is particularly/ntrue for genomes for which there is not a large collection of known gene sequences, such as the/nrecently published chicken genome. We used the chicken sequence to test comparative and/nhomology-based gene-finding methods followed by experimental validation as an effective genome/nannotation method./nResults: We performed experimental evaluation by RT-PCR of three different computational gene/nfinders, Ensembl, SGP2 and TWINSCAN, applied to the chicken genome. A Venn diagram was/ncomputed and each component of it was evaluated. The results showed that de novo comparative/nmethods can identify up to about 700 chicken genes with no previous evidence of expression, and/ncan correctly extend about 40% of homology-based predictions at the 5' end./nConclusions: De novo comparative gene prediction followed by experimental verification is/neffective at enhancing the annotation of the newly sequenced genomes provided by standard/nhomology-based methods.en
- dc.description.sponsorship This work was supported by grants from the Jérôme Lejeune,/nChildcare and Désirée and Niels Yde Foundations, the European Union, the/nSwiss National Science Foundation and the NCCR Frontiers in Genetics. E/nEyras is funded by the Institució Catalana de Recerca I Estudis Avançats/n(ICREA). R Guigo's lab acknowledges support from grants from the/nNational Plan for R&D (Spain), QLK3-CT-2002-02062 from the European/nCommunity and HG003150-01 from the National Institutes of Health./nResearch on gene prediction by vertebrate genome comparison in the/nBrent lab is supported by grant R01 HG02278 from the National Institutes/nof Health. This work was also supported by EMBL and the Wellcome Trust.en
- dc.format.mimetype application/pdfca
- dc.identifier.citation Eyras E, Reymond A, Castelo R, Bye J M, Cámara F, Flicek P, Huckle E J, Parra G, Shteynberg D D, Wyss C, Rogers J, Antonarakis S E, Birney E, Guigó R, Brent M R. Gene finding in the chicken genome. BMC Bioinformatics. 2005;6:131. DOI: 10.1186/1471-2105-6-131
- dc.identifier.doi http://dx.doi.org/10.1186/1471-2105-6-131
- dc.identifier.issn 1471-2105
- dc.identifier.uri http://hdl.handle.net/10230/13154
- dc.language.iso engca
- dc.publisher BioMed Centralca
- dc.relation.ispartof BMC Bioinformatics. 2005;6:131
- dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/003150
- dc.rights © 2005 Eyras et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This article is available from: http://www.biomedcentral.com/1471-2105/6/131ca
- dc.rights.accessRights info:eu-repo/semantics/openAccessen
- dc.rights.uri http://creativecommons.org/licenses/by/2.0
- dc.subject.keyword Animalsen
- dc.subject.keyword Chickensen
- dc.subject.keyword Exonsen
- dc.subject.keyword Intronsca
- dc.subject.keyword DNA Primersen
- dc.subject.keyword cDNAen
- dc.subject.keyword DNA sequence analysisen
- dc.subject.keyword Reverse Transcriptase Polymerase Chain Reactionen
- dc.subject.other Biologia computacional -- Mètodesca
- dc.subject.other Genòmica -- Bases de dadesca
- dc.subject.other Genòmica -- Models estadísticsca
- dc.subject.other Genètica -- Tècnicaca
- dc.subject.other Seqüència d'aminoàcidsca
- dc.title Gene finding in the chicken genomeca
- dc.type info:eu-repo/semantics/articleca
- dc.type.version info:eu-repo/semantics/publishedVersionen