This is a preview of subscription content, log in via an institution to check access.
References
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.
Delcher AL, Bratke KA, et al. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007;23(6):673–9.
Hoff KJ, Tech M, et al. Gene prediction in metagenomic fragments: a large scale machine learning approach. BMC Bioinformatics. 2008;9:217.
Hu G, Liu Y, et al. New solutions of translation initiation site prediction for prokaryotic genomes. Prog Biochem Biophys. 2008a;35(11):1254–62.
Hu G, Zheng X, et al. Computational evaluation of TIS annotation for prokaryotic genomes. BMC Bioinformatics. 2008b;9:160.
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.
Hu G, Guo J, et al. MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction. Bioinformatics. 2009a;25(14):1843–5.
Hu G, Zheng X, et al. Prediction of translation initiation site for microbial genomes with TriTISA. Bioinformatics. 2009b;25(1):123–5.
Hyatt D, Chen GL, et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119.
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.
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.
Nielsen P, Krogh A. Large-scale prokaryotic gene prediction and comparison to genome annotation. Bioinformatics. 2005;21(24):4322–9.
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.
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.
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.
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.
Tech M, Pfeifer N, et al. TICO: a tool for improving predictions of prokaryotic translation initiation sites. Bioinformatics. 2005;21(17):3568–9.
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.
Zhu H, Hu G, et al. Accuracy improvement for identifying translation initiation sites in microbial genomes. Bioinformatics. 2004;20(18):3308–17.
Zhu W, Lomsadze A, et al. Ab initio gene identification in metagenomic sequences. Nucleic Acids Res. 2010;38(12):e132.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media New York
About this entry
Cite this entry
Zhu, H., Hu, G. (2013). MetaTISA: Metagenomic Gene Start Prediction with. In: Nelson, K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6418-1_240-4
Download citation
DOI: https://doi.org/10.1007/978-1-4614-6418-1_240-4
Received:
Accepted:
Published:
Publisher Name: Springer, New York, NY
Online ISBN: 978-1-4614-6418-1
eBook Packages: Springer Reference Biomedicine and Life SciencesReference Module Biomedical and Life Sciences