Evaluation of gene-finding programs on mammalian sequences - PubMed (original) (raw)

Comparative Study

Evaluation of gene-finding programs on mammalian sequences

S Rogic et al. Genome Res. 2001 May.

Abstract

We present an independent comparative analysis of seven recently developed gene-finding programs: FGENES, GeneMark.hmm, Genie, Genescan, HMMgene, Morgan, and MZEF. For evaluation purposes we developed a new, thoroughly filtered, and biologically validated dataset of mammalian genomic sequences that does not overlap with the training sets of the programs analyzed. Our analysis shows that the new generation of programs has substantially better results than the programs analyzed in previous studies. The accuracy of the programs was also examined as a function of various sequence and prediction features, such as G + C content of the sequence, length and type of exons, signal type, and score of the exon prediction. This approach pinpoints the strengths and weaknesses of each individual program as well as those of computational gene-finding in general. The dataset used in this analysis (HMR195) as well as the tables with the complete results are available at http://www.cs.ubc.ca/\~rogic/evaluation/.

PubMed Disclaimer

Similar articles

• Evaluation of gene-finding algorithms by a content-balancing accuracy index.
  Zhang CT, Zhang R. Zhang CT, et al. J Biomol Struct Dyn. 2002 Jun;19(6):1045-52. doi: 10.1080/07391102.2002.10506807. J Biomol Struct Dyn. 2002. PMID: 12023806
• Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences.
  Pavy N, Rombauts S, Déhais P, Mathé C, Ramana DV, Leroy P, Rouzé P. Pavy N, et al. Bioinformatics. 1999 Nov;15(11):887-99. doi: 10.1093/bioinformatics/15.11.887. Bioinformatics. 1999. PMID: 10743555
• Improving gene recognition accuracy by combining predictions from two gene-finding programs.
  Rogic S, Ouellette BF, Mackworth AK. Rogic S, et al. Bioinformatics. 2002 Aug;18(8):1034-45. doi: 10.1093/bioinformatics/18.8.1034. Bioinformatics. 2002. PMID: 12176826
• Using MZEF to find internal coding exons.
  Zhang MQ. Zhang MQ. Curr Protoc Bioinformatics. 2002 Aug;Chapter 4:Unit 4.2. doi: 10.1002/0471250953.bi0402s00. Curr Protoc Bioinformatics. 2002. PMID: 18792940 Review.
• An Experimental Approach to Genome Annotation: This report is based on a colloquium sponsored by the American Academy of Microbiology held July 19-20, 2004, in Washington, DC.
  [No authors listed] [No authors listed] Washington (DC): American Society for Microbiology; 2004. Washington (DC): American Society for Microbiology; 2004. PMID: 33001599 Free Books & Documents. Review.

Cited by

• First Steps in the Analysis of Prokaryotic Pan-Genomes.
  Costa SS, Guimarães LC, Silva A, Soares SC, Baraúna RA. Costa SS, et al. Bioinform Biol Insights. 2020 Aug 7;14:1177932220938064. doi: 10.1177/1177932220938064. eCollection 2020. Bioinform Biol Insights. 2020. PMID: 32843837 Free PMC article. Review.
• A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms.
  Scalzitti N, Jeannin-Girardon A, Collet P, Poch O, Thompson JD. Scalzitti N, et al. BMC Genomics. 2020 Apr 9;21(1):293. doi: 10.1186/s12864-020-6707-9. BMC Genomics. 2020. PMID: 32272892 Free PMC article.
• Exon prediction based on multiscale products of a genomic-inspired multiscale bilateral filtering.
  Zhang X, Pan W. Zhang X, et al. PLoS One. 2019 Mar 21;14(3):e0205050. doi: 10.1371/journal.pone.0205050. eCollection 2019. PLoS One. 2019. PMID: 30897105 Free PMC article.
• An optimized approach for annotation of large eukaryotic genomic sequences using genetic algorithm.
  Chowdhury B, Garai A, Garai G. Chowdhury B, et al. BMC Bioinformatics. 2017 Oct 24;18(1):460. doi: 10.1186/s12859-017-1874-7. BMC Bioinformatics. 2017. PMID: 29065853 Free PMC article.
• Short Exon Detection via Wavelet Transform Modulus Maxima.
  Zhang X, Shen Z, Zhang G, Shen Y, Chen M, Zhao J, Wu R. Zhang X, et al. PLoS One. 2016 Sep 16;11(9):e0163088. doi: 10.1371/journal.pone.0163088. eCollection 2016. PLoS One. 2016. PMID: 27635656 Free PMC article.

References

1. 1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–410. - PubMed
2. 1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–3402. - PMC - PubMed
3. 1. Ashburner M, Mishra S, Roote J, Lewis SE, Blazej R, Davis T, Doyle C, Galle R, George R, Harris N, et al. An exploration of the sequence of a 2.9 Mb region of the genome of Drosophila melanogaster. The Adh region. Genetics. 1999;153:179–219. - PMC - PubMed
4. 1. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL. GenBank. Nucleic Acids Res. 2000;28:15–18. - PMC - PubMed
5. 1. Bernardi G. The isochore organization of the human genome and its evolutionary history — a review. Gene. 1993;135:57–66. - PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources

• Full Text Sources

  • Europe PubMed Central
  • HighWire
  • PubMed Central

• Other Literature Sources

  • The Lens - Patent Citations Database

• Medical

  • MedlinePlus Health Information

• Molecular Biology Databases

  • Saccharomyces Genome Database