Encyclopedia of Metagenomics

Living Edition
| Editors: Karen E. Nelson

MetaTISA: Metagenomic Gene Start Prediction with

  • Huaiqiu Zhu
  • Gangqing Hu
Living reference work entry
DOI: https://doi.org/10.1007/978-1-4614-6418-1_240-4

Synonyms

Definition

Gene start: the start position from which a genomic sequence can be translated into protein.

Introduction

Knowledge of exact information of gene start plays an important role in identification of native purified proteins from the high-throughput proteomics (Poole et al. 2005). In addition, a correct prediction of gene start facilitates the identification of cis-regulatory signals related to translation initiation (Hu et al. 2008c) and thus facilitates the understanding of the diversity and evolution scenario of translation initiation mechanisms (Zheng et al. 2011). However, gene start annotation in widely used public databases such as GenBank and RefSeq is not of high quality in general (Nielsen and Krogh 2005). In particular, the longest open reading frame is frequently used to annotate a protein-coding gene (Besemer et al. 2001), which results in a systematical low quality in gene start...

Keywords

Gene Start Phylogenetic Origin Metagenomic Sample Initial Annotation Longe Open Reading Frame 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
This is a preview of subscription content, log in to check access.

References

  1. Besemer J, Lomsadze A, et al. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res. 2001;29(12):2607–18.PubMedCentralPubMedCrossRefGoogle Scholar
  2. Delcher AL, Bratke KA, et al. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007;23(6):673–9.PubMedCentralPubMedCrossRefGoogle Scholar
  3. Hoff KJ, Tech M, et al. Gene prediction in metagenomic fragments: a large scale machine learning approach. BMC Bioinformatics. 2008;9:217.PubMedCentralPubMedCrossRefGoogle Scholar
  4. Hu G, Liu Y, et al. New solutions of translation initiation site prediction for prokaryotic genomes. Prog Biochem Biophys. 2008a;35(11):1254–62.Google Scholar
  5. Hu G, Zheng X, et al. Computational evaluation of TIS annotation for prokaryotic genomes. BMC Bioinformatics. 2008b;9:160.PubMedCentralPubMedCrossRefGoogle Scholar
  6. Hu G, Zheng X, et al. ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes. Nucleic Acids Res. 2008c;36(Database issue):D114–9.PubMedCentralPubMedGoogle Scholar
  7. Hu G, Guo J, et al. MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction. Bioinformatics. 2009a;25(14):1843–5.PubMedCrossRefGoogle Scholar
  8. Hu G, Zheng X, et al. Prediction of translation initiation site for microbial genomes with TriTISA. Bioinformatics. 2009b;25(1):123–5.PubMedCrossRefGoogle Scholar
  9. Hyatt D, Chen GL, et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119.PubMedCentralPubMedCrossRefGoogle Scholar
  10. Kelley DR, Liu B, et al. Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering. Nucleic Acids Res. 2012;40(1):e9.PubMedCentralPubMedCrossRefGoogle Scholar
  11. Makita Y, de Hoon MJ, et al. Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes. BMC Bioinformatics. 2007;8:47.PubMedCentralPubMedCrossRefGoogle Scholar
  12. Nielsen P, Krogh A. Large-scale prokaryotic gene prediction and comparison to genome annotation. Bioinformatics. 2005;21(24):4322–9.PubMedCrossRefGoogle Scholar
  13. Noguchi H, Taniguchi T, et al. MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res. 2008;15(6):387–96.PubMedCentralPubMedCrossRefGoogle Scholar
  14. Poole 2nd FL, Gerwe BA, et al. Defining genes in the genome of the hyperthermophilic archaeon Pyrococcus furiosus: implications for all microbial genomes. J Bacteriol. 2005;187(21):7325–32.PubMedCentralPubMedCrossRefGoogle Scholar
  15. Sandberg R, Winberg G, et al. Capturing whole-genome characteristics in short sequences using a naive Bayesian classifier. Genome Res. 2001;11(8):1404–9.PubMedCentralPubMedCrossRefGoogle Scholar
  16. Shine J, Dalgarno L. The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci U S A. 1974;71(4):1342–6.PubMedCentralPubMedCrossRefGoogle Scholar
  17. Tech M, Pfeifer N, et al. TICO: a tool for improving predictions of prokaryotic translation initiation sites. Bioinformatics. 2005;21(17):3568–9.PubMedCrossRefGoogle Scholar
  18. Zheng X, Hu G, et al. Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes. BMC Genomics. 2011;12:361.PubMedCentralPubMedCrossRefGoogle Scholar
  19. Zhu H, Hu G, et al. Accuracy improvement for identifying translation initiation sites in microbial genomes. Bioinformatics. 2004;20(18):3308–17.PubMedCrossRefGoogle Scholar
  20. Zhu W, Lomsadze A, et al. Ab initio gene identification in metagenomic sequences. Nucleic Acids Res. 2010;38(12):e132.PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  1. 1.Department of Biomedical Engineering, and Center for Theoretical BiologyPeking UniversityBeijingChina
  2. 2.Systems Biology Center, National Heart, Lung and Blood InstituteNational Institutes of HealthBethesdaUSA