Title:
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Gene finding in the chicken genome
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Author:
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Eyras Jiménez, Eduardo; Reymond, Alexandre; Castelo Valdueza, Robert; Bye, Jacqueline M.; Cámara, Francisco; Flicek, Paul; Huckle, Elizabeth J.; Parra Farré, Genís; Shteynberg, David D.; Wyss, Carine; Rogers, Jane; Antonarakis, Stylianos E.; Birney, Ewan; Brent, Michael R.; Guigó Serra, Roderic
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Other authors:
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Universitat Pompeu Fabra |
Abstract:
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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. |
Abstract:
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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. |
Subject(s):
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-Biologia computacional -- Mètodes -Genòmica -- Bases de dades -Genòmica -- Models estadístics -Genètica -- Tècnica -Seqüència d'aminoàcids -Animals -Chickens -Exons -DNA Primers -cDNA -DNA sequence analysis -Reverse Transcriptase Polymerase Chain Reaction -Introns |
Rights:
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© 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/1471-2105/6/131
http://creativecommons.org/licenses/by/2.0 |
Document type:
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Article Article - Published version |
Published by:
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BioMed Central
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