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 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.
Eyras
Eduardo
E
Institut Municipal d'Investigacio Medica, Universitat Pompeu Fabra, Centre de Regulacio Genomica, E08003 Barcelona, Catalonia, Spain. eeyras@imim.es
Reymond
Alexandre
A
Castelo
Robert
R
Bye
Jacqueline M
JM
Camara
Francisco
F
Flicek
Paul
P
Huckle
Elizabeth J
EJ
Parra
Genis
G
Shteynberg
David D
DD
Wyss
Carine
C
Rogers
Jane
J
Antonarakis
Stylianos E
SE
Birney
Ewan
E
Guigo
Roderic
R
Brent
Michael R
MR
D000818:Animals; D002645:Chickens; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods*; D017931:DNA Primers; D018076:DNA, Complementary / Q000378:metabolism; D003627:Data Interpretation, Statistical; D030541:Databases, Genetic; D005091:Exons; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D016678:Genome; D007438:Introns; D015233:Models, Statistical; D020133:Reverse Transcriptase Polymerase Chain Reaction; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software; D014018:Tissue Distribution
D017931:DNA Primers; D018076:DNA, Complementary