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Evaluation of five ab initio gene prediction programs for the discovery of maize genes

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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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Abbreviations

AE:

actual exon

CC:

correlation coefficient

FN:

false negative

FP:

false positive

GSSs:

genome survey sequences

HC:

high C o t

MAGIs:

maize assembled genomic islands

ME:

missing exon

MF:

methylation filtration

OE:

overlapped exon

PE:

partial exon

RACE:

Rapid Amplification of cDNA Ends

SN:

sensitivity

SP:

specificity

TE:

true exon

TP:

true positive

WE:

wrong exon

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Author information

Author notes

  1. Xiangqin Cui

    Present address: Department of Biostatistics, Birmingham, AL, 35294, USA

Authors and Affiliations

  1. Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa, 50011-3650

    Hong Yao, Ling Guo, Yan Fu, Lisa A. Borsuk, David S. Skibbe, Xiangqin Cui, Jun Cao & Patrick S. Schnable

  2. Department of Agronomy, Iowa State University, Ames, Iowa, 50011-3650

    Tsui-Jung Wen & Patrick S. Schnable

  3. Department of Mathematics, Iowa State University, Ames, Iowa, 50011-3650

    Daniel A. Ashlock

  4. Inderdepartmental Graduate Programs in Genetics, Iowa State University, Ames, Iowa, 50011-3650

    Hong Yao, Yan Fu, Xiangqin Cui, Jun Cao & Patrick S. Schnable

  5. Department of Molecular, Cellular and Developmental Biology, Iowa State University, Ames, Iowa, 50011-3650

    David S. Skibbe & Patrick S. Schnable

  6. Department of Electrical and Computer Engineering and Department of Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa, 50011-3650

    Ling Guo, Lisa A. Borsuk, Scott J. Emrich, Daniel A. Ashlock & Patrick S. Schnable

  7. Center for Plant Genomics, Iowa State University, Ames, Iowa, 50011-3650

    Patrick S. Schnable

  8. Mid South Area Genomics Facility, USDA-ARS, Stoneville, MS, 38776-0038, USA

    Brian E. Scheffler

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  1. Hong Yao
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  2. Ling Guo
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  3. Yan Fu
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  9. Jun Cao
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  10. Scott J. Emrich
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Corresponding author

Correspondence to Patrick S. Schnable.

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†these authors contributed equally to this work

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Yao, H., Guo, L., Fu, Y. et al. Evaluation of five ab initio gene prediction programs for the discovery of maize genes. Plant Mol Biol 57, 445–460 (2005). https://doi.org/10.1007/s11103-005-0271-1

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  • DOI: https://doi.org/10.1007/s11103-005-0271-1

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