title: Gene finding in the chicken genome.
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.
authors.affiliation: Institut Municipal d'Investigacio Medica, Universitat Pompeu Fabra, Centre de Regulacio Genomica, E08003 Barcelona, Catalonia, Spain. eeyras@imim.es
authors.forename: Eduardo
authors.initials: E
authors.lastname: Eyras
authors.forename: Alexandre
authors.initials: A
authors.lastname: Reymond
authors.forename: Robert
authors.initials: R
authors.lastname: Castelo
authors.forename: Jacqueline M
authors.initials: JM
authors.lastname: Bye
authors.forename: Francisco
authors.initials: F
authors.lastname: Camara
authors.forename: Paul
authors.initials: P
authors.lastname: Flicek
authors.forename: Elizabeth J
authors.initials: EJ
authors.lastname: Huckle
authors.forename: Genis
authors.initials: G
authors.lastname: Parra
authors.forename: David D
authors.initials: DD
authors.lastname: Shteynberg
authors.forename: Carine
authors.initials: C
authors.lastname: Wyss
authors.forename: Jane
authors.initials: J
authors.lastname: Rogers
authors.forename: Stylianos E
authors.initials: SE
authors.lastname: Antonarakis
authors.forename: Ewan
authors.initials: E
authors.lastname: Birney
authors.forename: Roderic
authors.initials: R
authors.lastname: Guigo
authors.forename: Michael R
authors.initials: MR
authors.lastname: Brent
mesh_terms: 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
chemical_list: D017931:DNA Primers; D018076:DNA, Complementary