MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction

Bioinformatics

Volumn 25, Issue 14, 2009, Pages 1843-1845

  Hu, Gang Qing ^a   Guo, Jiang Tao ^a   Liu, Yong Chu ^a   Zhu, Huaiqiu ^a  

^a PEKING UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER SYSTEM; GENE CLUSTER; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC ANALYSIS; INFORMATION PROCESSING; METAGENOMICS; PHYLOGENY; PRIORITY JOURNAL; TRANSLATION INITIATION;

GENES; GENOMICS; PEPTIDE CHAIN INITIATION, TRANSLATIONAL; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 67649884742     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp272     Document Type: Article

References (27)

1. Aivaliotis,M. et al. (2007) Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis. J. Proteome Res., 6, 2195-2204.
2. Besemer,J. et al. (2001) GeneMarkS: A self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res., 29 2607-2618.
3. Delcher,A.L. et al. (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics, 23, 673-679.
4. Diaz,N.N. et al. (2009) TACOA: Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinformatics, 10, 56.
5. Garcia-Vallve,S. et al. (2003) HGT-DB: A database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Res., 31, 187-189.
6. Gill,S.R. et al. (2006) Metagenomic analysis of the human distal gut microbiome. Science, 312, 1355-1359.
7. Hoff,K.J. et al. (2008) Gene prediction in metagenomic fragments: a large scale machine learning approach. BMC Bioinformatics, 9 217.
8. Hu,G.-Q. et al. (2008a) ProTISA: A comprehensive resource for translation initiation site annotation in prokaryotic genomes. Nucleic Acids Res., 36, D114-D119.
9. Hu,G.-Q. et al. (2008b) Computational evaluation of TIS annotation for prokaryotic genomes. BMC Bioinformatics, 9, 160.
10. Hu,G.-Q. et al. (2009) Prediction of translation initiation site for microbial genomes with TriTISA. Bioinformatics, 25, 123-125.
11. Ma,J. et al. (2002) Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures. J. Bacteriol., 184, 5733-5745.
12. Makita,Y. et al. (2007) Hon-yaku: A biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes. BMC Bioinformatics, 8, 47.
13. McHardy,A.C. et al. (2007) Accurate phylogenetic classification of variable-length DNA fragments. Nat. Methods, 4, 63-72.
14. Médigue,C. et al. (1991) Evidence for horizontal gene transfer in Escherichia coli speciation. J. Mol. Biol., 222, 851-856.
15. Nakamoto,T. (2009) Evolution and the universality of the mechanism of initiation of protein synthesis. Gene, 432, 1-6.
16. Nielsen,P. and Krogh,A. (2005) Large-scale prokaryotic gene prediction and comparison to genome annotation. Bioinformatics, 21, 4322-4329.
17. Noguchi,H. et al. (2006) MetaGene: Prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Res., 34 5623-5630.
18. Noguchi,H. et al. (2008) MetaGeneAnnotator: Detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res., 15, 387-396.
19. Podell,S. and Gaasterland,T. (2007) DarkHorse: Amethod for genome-wide prediction of horizontal gene transfer. Genome Biol., 8, R16.
20. Rudd,K.E. (2000) EcoGene: A genome sequence database for Escherichia coli K-12. Nucleic Acids Res., 28, 60-64.
21. Sandberg,R. et al. (2001) Capturing whole-genome characteristics in short sequences using a naive Bayesian classifier. Genome Res., 11, 1404-1409.
22. Sazuka,T. et al. (1999) Cyano2Dbase updated: Linkage of 234 protein spots to corresponding genes through N-terminal microsequencing. Electrophoresis, 20, 2160-2171.
23. Tamames,J. and Moya,A. (2008) Estimating the extent of horizontal gene transfer in metagenomic sequences. BMC Genomics, 9, 136.
24. Tech,M. et al. (2005) TICO: A tool for improving predictions of prokaryotic translation initiation sites. Bioinformatics, 21 3568-3569.
25. Yada,T. et al. (2001) A novel bacterial gene-finding system with improved accuracy in locating start codons. DNA Res., 8, 97-106.
26. Yamazaki,S. et al. (2006) Proteome analysis of an aerobic hyper-thermophilic crenarchaeon Aeropyrum pernix K1. Mol. Cell. Proteomics, 5, 811-823.
27. Zhu,H.Q. et al. (2004) Accuracy improvement for identifying translation initiation sites in microbial genomes. Bioinformatics, 20, 3308-3317.