Detecting LTR structures in human genomic sequences using profile hidden Markov models

Expert Systems with Applications

Volumn 36, Issue 1, 2009, Pages 668-674

  Wu, Li Ching ^a   Huang, Hsien Da ^b   Chang, Yu Chung ^c   Lee, Ying Chun ^a   Horng, Jorng Tzong ^a  

^a NATIONAL CENTRAL UNIVERSITY   (Taiwan)

^b NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

^c MING CHUAN UNIVERSITY   (Taiwan)

Author keywords

Genome; Hidden Markov model; LTR; Repeats; Transposable elements

Indexed keywords

ABS RESINS; LEARNING SYSTEMS; MARKOV PROCESSES; OBJECT RECOGNITION; SENSOR NETWORKS; WAVELET TRANSFORMS;

GENOME; HIDDEN MARKOV MODEL; LTR; REPEATS; TRANSPOSABLE ELEMENTS;

HIDDEN MARKOV MODELS;

EID: 53849129991     PISSN: 09574174     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.eswa.2007.10.045     Document Type: Article

References (17)

1. Bailey T.L., and Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings of the International Conference Intelligent System for Molecular Biology 2 (1994) 28-36
2. Brown T.A. In: Kingston F. (Ed). The repetitive DNA content of genomes (1999), John Weley, New York 138
3. Eddy S.R. Profile hidden Markov models. Bioinformatics 14 9 (1998) 755-763
4. Frech K., Danescu-Mayer J., et al. A novel method to develop highly specific models for regulatory units detects a new LTR in GenBank which contains a functional promoter. Journal of Molecular Biology 270 5 (1997) 674-687
5. Han J., and Kamber M. Clustering analysis. Data mining concepts and techniques (2001), Morgan Kaufman 335
6. Hubbard T., Barker D., et al. The Ensembl genome database project. Nucleic Acids Research 30 1 (2002) 38-41
7. Hughes J.D., Estep P.W., et al. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. Journal of Molecular Biology 296 5 (2000) 1205-1214
8. Juretic N., Bureau T.E., et al. Transposable element annotation of the rice genome. Bioinformatics 20 2 (2004) 155-160
9. Jurka J. Repeats in genomic DNA: mining and meaning. Current Opinion Structural Biology 8 3 (1998) 333-337
10. Jurka J. Repbase update: a database and an electronic journal of repetitive elements. Trends Genetics 16 9 (2000) 418-420
11. Kazazian Jr. H.H. Mobile elements and disease. Current Opinion Genetic and Development 8 3 (1998) 343-350
12. Li W.H., Gu Z., et al. Evolutionary analyses of the human genome. Nature 409 6822 (2001) 847-849
13. McCarthy E.M., Liu J., et al. Long terminal repeat retrotransposons of Oryza sativa. Genome Biology 3 10 (2002) RESEARCH0053
14. McCarthy E.M., and McDonald J.F. LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics 19 3 (2003) 362-367
15. McCarthy E.M., and McDonald J.F. Long terminal repeat retrotransposons of Mus musculus. Genome Biology 5 3 (2004) R14
16. Smit A.F. Identification of a new, abundant superfamily of mammalian LTR-transposons. Nucleic Acids Research 21 8 (1993) 1863-1872
17. Zhang X., and Wessler S.R. Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea. Proceedings of the National Academy of Sciences of the USA 101 15 (2004) 5589-5594