Translation initiation start prediction in human cDNAs with high accuracy

被引:57
作者
Hatzigeorgiou, AG
机构
[1] Metagen GmbH, D-14195 Berlin, Germany
[2] Synapt Ltd, Iraklion 71110, Greece
关键词
D O I
10.1093/bioinformatics/18.2.343
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Motivation: Correct identification of the Translation Initiation Start (TIS) in cDNA sequences is an important issue for genome annotation. The aim of this work is to improve upon current methods and provide a performance guaranteed prediction. Methods: This is achieved by using two modules, One sensitive to the conserved motif and the other sensitive to the coding/non-coding potential around the start codon. Both modules are based on Artificial Neural Networks (ANNs). By applying the simplified method of the ribosome scanning model, the algorithm starts a linear search at, the beginning of the coding ORF and stops once the combination of the two modules predicts a positive score. Results: According to the results of the test group, 94% of the TIS were correctly predicted. A confident decision is obtained through the use of the Las Vegas algorithm idea. The incorporation of this algorithm leads to a highly accurate recognition of the TIS in human cDNAs for 60% of the cases.
引用
收藏
页码:343 / 350
页数:8
相关论文
共 21 条
[1]  
Agarwal P., 1998, Proceedings of the Second Annual International Conference on Computational Molecular Biology, RECOMB '98, P2
[2]  
AGARWAL P, 1998, P 2 ANN INT C COMP M, P1
[3]  
Brassard G, 1996, FUNDAMENTALS ALGORIT
[4]   PREDICTION OF HUMAN MESSENGER-RNA DONOR AND ACCEPTOR SITES FROM THE DNA-SEQUENCE [J].
BRUNAK, S ;
ENGELBRECHT, J ;
KNUDSEN, S .
JOURNAL OF MOLECULAR BIOLOGY, 1991, 220 (01) :49-65
[5]   Isolation and characterization of a mammalian homolog of the Drosophila white gene [J].
Croop, JM ;
Tiller, GE ;
Fletcher, JA ;
Lux, ML ;
Raab, E ;
Goldenson, D ;
Son, D ;
Arciniegas, S ;
Wu, RL .
GENE, 1997, 185 (01) :77-85
[6]  
Fahlman S., 1990, ADV NEURAL INFORMATI, V2, P524
[7]  
Hatzigeorgiou A, 1999, CONCUR SYST ENGN SER, V54, P148
[8]  
HATZIGEORGIOU A, 1999, P INT JOINT C NEUR N
[9]   AN ANALYSIS OF 5'-NONCODING SEQUENCES FROM 699 VERTEBRATE MESSENGER-RNAS [J].
KOZAK, M .
NUCLEIC ACIDS RESEARCH, 1987, 15 (20) :8125-8148
[10]   Interpreting cDNA sequences: Some insights from studies on translation [J].
Kozak, M .
MAMMALIAN GENOME, 1996, 7 (08) :563-574