Eyras Jiménez, EduardoReymond, AlexandreCastelo Valdueza, RobertBye, Jacqueline M.Cámara, FranciscoFlicek, PaulHuckle, Elizabeth J.Parra Farré, GenísShteynberg, David D.Wyss, CarineRogers, JaneAntonarakis, Stylianos E.Birney, EwanGuigó Serra, RodericBrent, Michael R.2011-11-282011-11-282005Eyras 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: 10.1186/1471-2105-6-1311471-2105http://hdl.handle.net/10230/13154Background: 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.application/pdfeng© 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/1471-2105/6/131Biologia computacional -- MètodesGenòmica -- Bases de dadesGenòmica -- Models estadísticsGenètica -- TècnicaSeqüència d'aminoàcidsinfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1186/1471-2105-6-131AnimalsChickensExonsIntronsDNA PrimerscDNADNA sequence analysisReverse Transcriptase Polymerase Chain Reactioninfo:eu-repo/semantics/openAccess