Dragon TIS Spotter: An Arabidopsis-derived predictor of translation initiation sites in plants

Bioinformatics

Volumn 29, Issue 1, 2013, Pages 117-118

  Magana Mora, Arturo ^a   Ashoor, Haitham ^a   Jankovic, Boris R ^a   Kamau, Allan ^a   Awara, Karim ^a   Chowdhary, Rajesh ^b   Archer, John A C ^a   Bajic, Vladimir B ^a  

^a KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Saudi Arabia)

^b MARSHFIELD CLINIC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA; EUKARYOTA; POPULUS TRICHOCARPA; VITACEAE; VITIS VINIFERA;

ARABIDOPSIS; ARTICLE; ARTIFICIAL NEURAL NETWORK; COMPUTER PROGRAM; DNA SEQUENCE; GENETICS; GENOMICS; INTERNET; NUCLEOTIDE MOTIF; PLANT GENOME; RNA TRANSLATION; SENSITIVITY AND SPECIFICITY;

ARABIDOPSIS; GENOME, PLANT; GENOMICS; INTERNET; NEURAL NETWORKS (COMPUTER); NUCLEOTIDE MOTIFS; PEPTIDE CHAIN INITIATION, TRANSLATIONAL; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84871809324     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts638     Document Type: Article

References (18)

1. Do, J.H. and Choi, D.K. (2006) Computational approaches to gene prediction. J. Microbiol., 44, 137-144. (Pubitemid 44874788)
2. Hann, S.R. (1994) Regulation and function of non-AUG-initiated protooncogenes. Biochimie, 76, 880-886.
3. Kozak, M. (1989) Context effects and inefficient initiation at non-AUG codons in eucaryotic cell-free translation systems. Mol. Cell. Biol., 9, 5073-5080. (Pubitemid 19275978)
4. Li, G. et al. (2004) Translation initiation sites prediction with mixture gaussian models. In: Jonassen, I. and Kim, J. (eds) WABI 2004, LNBI 3240. Springer-Velrag, Berling Heidelberg, pp. 338-349. (Pubitemid 39750021)
5. Li, G.L. and Leong, T.Y. (2005) Feature selection for the prediction of translation initiation sites. Genomics Proteomics Bioinformatics, 3, 73-83.
6. Liu, H. et al. (2004) Using amino acid patterns to accurately predict translation initiation sites. In Silico Biol., 4, 255-269. (Pubitemid 39600475)
7. Liu, H. and Wong, L. (2003) Data mining tools for biological sequences. J. Bioinform. Comput. Biol., 1, 139-167.
8. Ma, C. et al. (2006) Feature mining integration for improving the prediction accuracy of translation initiation sites in eukaryotic mRNAs. In Fifth International Conference on Grid and Cooperative Computing Workshops. IEEE Computer Society, Washington DC, pp. 349-356.
9. Pedersen, A.G. and Nielsen, H. (1997) Neural network prediction of translation initiation sites in eukaryotes perspectives for EST and genome analysis. In Proceedings 5th International Conference on Intelligent Systems for Molecular Biology. pp. 226-233.
10. Pertea, M. and Salzberg, S. (2002) A method to improve the performance of translation start site detection and its application for gene finding. In: Guigo, R. and Gusfield, D. (eds.) WABI 2002, LNCS 2452. Springer-Verlag, Berlin Heidelberg, pp. 210-219.
11. Prechelt, L. (1998) Early stopping-but when?. In: Orr, G.B. and Muller, K.R. (eds.) Neural Networks: Tricks of the Trade, LNCS 1524 Springer-Verlag, Berlin Heidelberg. pp. 55-69.
12. Preiss, T. and Hentze, M. (2003) Starting the protein synthesis machine: eukaryotic translation initiation. Bioessays, 25, 1201-1211. (Pubitemid 37499320)
13. Rajapakse, J.C. and Ho, L.S. (2005) Markov encoding for detecting signals in genomic sequences. IEEE/ACM Trans. Comput. Biol. Bioinform., 2, 131-142.
14. Saeys, Y. et al. (2007) Translation initiation site prediction on a genomic scale: beauty of simplicity. Bioinformatics, 23, i418-i423. (Pubitemid 47244428)
15. Sparks, M.E. and Brendel, V. (2008) MetWAMer: eukaryotic translation initiation site prediction. BMC Bioinformatics, 9, 381.
16. Tikole, S. and Sankararamakrishnan, R. (2008) Prediction of translation initiation sites in human mRNA sequences with AUG start codon in weak Kozak context: a neural network approach. Biochem. Biophys. Res. Commn., 369, 1166-1168.
17. Tzanis, G. and Vlahavas, I. (2006) Prediction of translation initiation sites using classifier selection. Chapter in advances in artificial intelligence. In: Lecture Notes in Computer Science. Vol. 3955, Springer-Verlag, Berlin Heidelberg, pp. 367-377. (Pubitemid 44029997)
18. Zeng, F. et al. (2002) Using feature generation and feature selection for accurate prediction of translation initiation sites. Genome Inform., 13, 192-200.