A fast algorithm for the exhaustive analysis of 12-nucleotide-long DNA sequences. Applications to human genomics

Proceedings - International Parallel and Distributed Processing Symposium, IPDPS 2003

Volumn , Issue , 2003, Pages

  Arnau, Vicente ^a   Marín, Ignacio ^a  

^a UNIVERSITY OF VALENCIA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; APPLICATION PROGRAMS; BIOINFORMATICS; CHROMOSOMES; DISTRIBUTED PARAMETER NETWORKS; NUCLEOTIDES; PERSONAL COMPUTERS; SEARCH ENGINES;

CODING REGION; CONVENTIONAL DATABASE; DIFFERENT CLASS; FAST ALGORITHMS; HUMAN CHROMOSOMES; HUMAN GENOMICS; TANDEM REPEATS;

DNA SEQUENCES;

EID: 84947217347     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IPDPS.2003.1213287     Document Type: Conference Paper

References (17)

1. S. Karlin, A. M. Campbell, J. Mrázek. Comparative DNA analysis across diverse genomes. Annu. Rev. Genet., 32:185-225 (1998).
2. A. J. Gentles, S. Karlin. Genome-scale compositional comparisons in eukaryotes. Genome Res., 11:540-546 (2001).
3. E. Uberbacher, R. Mural. Locating protein coding regions in human DNA sequences by a multiple sensor-neural network approach. Proc Natl. Acad. Sci. USA, 388:11261-11265 (1991).
4. E. Zinder, G. Stormo. Identification of coding regions in genomic DNA sequences: An application of dynamic programming and neural netwoks. Nucleic Acids Res., 21:607-613 (1993).
5. V. Solovyev, A. Salamov, C. Lawrence. Predicting internal exons by oligonucleotide composition and discriminant analysis of sliceable open reading frames. Nucleic Acids Res., 22:5156-5163. (1994).
6. D. Prestridge. Predicting pol II promoter sequences using transcription factor binding sites. J. Mol. Biol., 249:923-932. (1995).
7. Q. Chen, G. Hertz, G. Stormo. PromFD 1. 0: A computer program that predicts eukaryotic pol II promoters using strings and IMD matrices. Comput. Applic. Biosci., 13:29-35 (1997).
8. A. Brazma, I. Jonassen, J. Vilo, E. Ukkonen. Predicting gene regulatory elemetns in silico on a genomic scale. Genome Res., 8:1202-1215 (1998).
9. J. van Helden, B. André, J. Collado-Vives. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol., 281:827-842 (1998).
10. S. Karlin, J. Mrázek. Compositional differences within and between eukaryotic genomes. Proc. Natl. Acad. Sci. USA, 94:10227-10232 (1997).
11. I. Dunham, N. Shimizu, B. A. Roe, S. Chissoe, et al. The DNA sequence of human chromosome 22. Nature, 402:489-495 (1999).
12. M. Hattori, A. Fujiyama, T. D. Taylor, H. Watanabe et al. The DNA sequence of human chromosome 21. Nature, 405:311-319 (2000).
13. P. Kapranov, S. E. Cawley, J. Drenkow, S. Bekiranov, R. L. Strausberg, S. P. A. Fodor, T. R. Gingeras. Large-scale transcriptional activity in chromosomes 21 and 22. Science, 296:916-919 (2002)
14. Ch. Chen, A. J. Gentles, J. Jurka, S. Karlin. Genes, pseudogenes, and Alu sequence organization across human chromosomes 21 and 22. Proc. Natl. Acad. Sci. USA, 99:2930-2935 (2002).
15. P. Baldi, S. Brunak. Bioinformatics. The Machine Learning Approach., Second Edition. A Bradford Book. The MIT Press. (2001).
16. R. Durbin, S. R. Eddy, A. Krogh, G. Mitchison. Biological sequence analysis. Probabilistic models of proteins and nucleic acids, Cambridge University Press, Cambridge (1998).
17. J. L. Desseyn, J. P. Aubert, N. Porchet, A. Laine. Evolution of the large secreted gel-forming mucins. Mol. Biol. Evol., 17:1175-1184 (2000).