Gene finding in the chicken genome

Background: Despite the continuous production of genome sequence for a number of organisms,reliable, comprehensive, and cost effective gene prediction remains problematic. This is particularlytrue for genomes for which there is not a large collection of known gene sequences, such as therecently published chicken genome. We used the chicken sequence to test comparative andhomology-based gene-finding methods followed by experimental validation as an effective genomeannotation method.Results: We performed experimental evaluation by RT-PCR of three different computational genefinders, Ensembl, SGP2 and TWINSCAN, applied to the chicken genome. A Venn diagram wascomputed and each component of it was evaluated. The results showed that de novo comparativemethods can identify up to about 700 chicken genes with no previous evidence of expression, andcan correctly extend about 40% of homology-based predictions at the 5' end.Conclusions: De novo comparative gene prediction followed by experimental verification iseffective at enhancing the annotation of the newly sequenced genomes provided by standardhomology-based methods.

This work was supported by grants from the Jérôme Lejeune,Childcare and Désirée and Niels Yde Foundations, the European Union, theSwiss National Science Foundation and the NCCR Frontiers in Genetics. EEyras is funded by the Institució Catalana de Recerca I Estudis Avançats(ICREA). R Guigo's lab acknowledges support from grants from theNational Plan for R&D (Spain), QLK3-CT-2002-02062 from the EuropeanCommunity and HG003150-01 from the National Institutes of Health.Research on gene prediction by vertebrate genome comparison in theBrent lab is supported by grant R01 HG02278 from the National Institutesof Health. This work was also supported by EMBL and the Wellcome Trust.