TY - JOUR
T1 - Gene finding in the chicken genome
AU - Eyras, Eduardo
AU - Reymond, Alexandre
AU - Castelo, Robert
AU - Bye, Jacqueline M.
AU - Camara, Francisco
AU - Flicek, Paul
AU - Huckle, Elizabeth J.
AU - Parra, Genis
AU - Shteynberg, David D.
AU - Wyss, Carine
AU - Rogers, Jane
AU - Antonarakis, Stylianos E.
AU - Birney, Ewan
AU - Guigo, Roderic
AU - Brent, Michael R.
PY - 2005/5/30
Y1 - 2005/5/30
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=25444516195&partnerID=8YFLogxK
U2 - 10.1186/1471-2105-6-131
DO - 10.1186/1471-2105-6-131
M3 - Article
C2 - 15924626
AN - SCOPUS:25444516195
SN - 1471-2105
VL - 6
JO - BMC bioinformatics
JF - BMC bioinformatics
M1 - 131
ER -