{"doi":"10.1186/1471-2105-6-131","title":"Gene finding in the chicken genome","abstract":"<jats:title>Abstract</jats:title><jats:sec>\n                        <jats:title>Background</jats:title>\n                        <jats:p>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.</jats:p>\n                     </jats:sec><jats:sec>\n                        <jats:title>Results</jats:title>\n                        <jats:p>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 <jats:italic>de novo</jats:italic> 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.</jats:p>\n                     </jats:sec><jats:sec>\n                        <jats:title>Conclusions</jats:title>\n                        <jats:p><jats:italic>De novo</jats:italic> comparative gene prediction followed by experimental verification is effective at enhancing the annotation of the newly sequenced genomes provided by standard homology-based methods.</jats:p>\n                     </jats:sec>","journal":"BMC 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