ArticlePlant molecular biology2005
Evaluation of five ab initio gene prediction programs for the discovery of maize genes.
Article in Plant molecular biology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
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- Evidence-based gene models for structural and functional annotations of the oil palm genome.Biology direct · 2017Article
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- BuT2 is a member of the third major group of hAT transposons and is involved in horizontal transfer events in the genus Drosophila.Genome biology and evolution · 2014Article
- MEGANTE: a web-based system for integrated plant genome annotation.Plant & cell physiology · 2014Article
- Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application).BMC bioinformatics · 2013Article
- Isolation and diversity analysis of resistance gene homologues from switchgrass.G3 (Bethesda, Md.) · 2013Article
- Immunoglobulin genes of the turtles.Immunogenetics · 2013Article
- Mar, a MITE family of hAT transposons in Drosophila.Mobile DNA · 2012Article
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- Gene models from ESTs (GeneModelEST): an application on the Solanum lycopersicum genome.BMC bioinformatics · 2007Article
- Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.Genome research · 2007Article
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Five ab initio programs (FGENESH, GeneMark.hmm, GENSCAN, GlimmerR and Grail) were evaluated for their accuracy in predicting maize genes. Two of these programs, GeneMark.hmm and GENSCAN had been trained for maize; FGENESH had been trained for monocots (including maize), and the others had been trained for rice or Arabidopsis. Initial evaluations were conducted using eight maize genes (gl8a, pdc2, pdc3, rf2c, rf2d, rf2e1, rth1, and rth3) of which the sequences were not released to the public prior to conducting this evaluation. The significant advantage of this data set for this evaluation is that these genes could not have been included in the training sets of the prediction programs. FGENESH yielded the most accurate and GeneMark.hmm the second most accurate predictions. The five programs were used in conjunction with RT-PCR to identify and establish the structures of two new genes in the a1-sh2 interval of the maize genome. FGENESH, GeneMark.hmm and GENSCAN were tested on a larger data set consisting of maize assembled genomic islands (MAGIs) that had been aligned to ESTs. FGENESH, GeneMark.hmm and GENSCAN correctly predicted gene models in 773, 625, and 371 MAGIs, respectively, out of the 1353 MAGIs that comprise data set 2.
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