ArticleBMC bioinformatics2005
Gene finding in the chicken genome.
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Integrating physiological and multi-omics methods to elucidate heat stress tolerance for sustainable rice production.Physiology and molecular biology of plants : an international journal of functional plant biology · 2024Review
- From tradition to innovation: conventional and deep learning frameworks in genome annotation.Briefings in bioinformatics · 2024Review
- Multi-Omics and Integrative Approach towards Understanding Salinity Tolerance in Rice: A Review.Biology · 2022Review
- Functional annotation of differentially expressed fetal cardiac microRNA targets: implication for microRNA-based cardiovascular therapeutics.3 Biotech · 2018Article
- Genome Scan for Selection in Structured Layer Chicken Populations Exploiting Linkage Disequilibrium Information.PloS one · 2015Article
- Detecting and comparing non-coding RNAs in the high-throughput era.International journal of molecular sciences · 2013Review
- Re-annotation is an essential step in systems biology modeling of functional genomics data.PloS one · 2010Article
- The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species.BMC genomics · 2009Article
- A first-generation microsatellite-based genetic linkage map of the Siberian jay (Perisoreus infaustus): insights into avian genome evolution.BMC genomics · 2009Article
- A general definition and nomenclature for alternative splicing events.PLoS computational biology · 2008Article
- Targeted discovery of novel human exons by comparative genomics.Genome research · 2007Article
- Experimental validation of novel genes predicted in the un-annotated regions of the Arabidopsis genome.BMC genomics · 2007Article
- Characterising alternate splicing and tissue specific expression in the chicken from ESTs.Cytogenetic and genome research · 2007Article
- AgBase: a unified resource for functional analysis in agriculture.Nucleic acids research · 2007Article
- AgBase: a functional genomics resource for agriculture.BMC genomics · 2006Article
- ASGS: an alternative splicing graph web service.Nucleic acids research · 2006Article
- Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.Genome biology · 2006Article
- EGASP: the human ENCODE Genome Annotation Assessment Project.Genome biology · 2006Review
Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
backgroundDespite 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.
resultsWe 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.
conclusionsDe 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.
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