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Gene finding in the chicken genome

Eyras, Eduardo
Castelo, Robert
Bye, J. M.
Camara, Francisco
Flicek, Paul
Huckle, E. J.
Parra, Genis
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Published in BMC bioinformatics. 2005, vol. 6, 131
Abstract BACKGROUND: Despite the continuous production of genome sequence for a number of organisms, reliable, comprehensive, and cost effective gene prediction remains problematic. This is particularly true for genomes for which there is not a large collection of known gene sequences, such as the recently published chicken genome. We used the chicken sequence to test comparative and homology-based gene-finding methods followed by experimental validation as an effective genome annotation method. RESULTS: We performed experimental evaluation by RT-PCR of three different computational gene finders, Ensembl, SGP2 and TWINSCAN, applied to the chicken genome. A Venn diagram was computed and each component of it was evaluated. The results showed that de novo comparative methods can identify up to about 700 chicken genes with no previous evidence of expression, and can correctly extend about 40% of homology-based predictions at the 5' end. CONCLUSIONS: De novo comparative gene prediction followed by experimental verification is effective at enhancing the annotation of the newly sequenced genomes provided by standard homology-based methods.
Keywords AnimalsChickensChromosome MappingComputational Biology/ methodsDNA PrimersDNA, Complementary/metabolismData Interpretation, StatisticalDatabases, GeneticExonsExpressed Sequence TagsGene Expression ProfilingGenomeIntronsModels, StatisticalReverse Transcriptase Polymerase Chain ReactionSequence AlignmentSequence Analysis, DNASoftwareTissue Distribution
PMID: 15924626
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EYRAS, Eduardo et al. Gene finding in the chicken genome. In: BMC bioinformatics, 2005, vol. 6, p. 131. doi: 10.1186/1471-2105-6-131 https://archive-ouverte.unige.ch/unige:9169

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Deposited on : 2010-07-12

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