Finding intron/exon splice junctions using INFO, INterruption finder and organizer

Journal of Computational Biology

Volumn 5, Issue 2, 1998, Pages 307-321

  Laub, Michael T ^a,b   Smith, Douglas W ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b STANFORD UNIVERSITY   (United States)

Author keywords

DNA sequence analysis; Exons; Gene function; Genes; Introns; Prediction; Protein similarities; Sensitivity; Specificity; Splice junctions; Windowing algorithm

Indexed keywords

ALGORITHM; ARTICLE; DNA DETERMINATION; DNA SEQUENCE; EXON; HUMAN; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

EID: 0031878236     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.1998.5.307     Document Type: Article

References (23)

1. Altschul, S.F. 1991. Amino acid substitution matrices from an information theoric perspective. J. Mol. Biol. 219, 555-565.
2. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
3. Bairoch, A. 1992. PROSITE: A dictionary of sites and patterns in proteins. Nucl. Acids Res. 20, 2013-2018.
4. Borodovsky, M., and McIninch, J. 1993. GeneMark: parallel gene recognition for both DNA strands. Computers Chem. 17, 123-133.
5. Claverie, J.-M., and States, D.J. 1993. Information enhancement methods for large scale sequence analysis. Computers Chem. 17, 191-201.
6. Dayhoff, M.O. 1978. In Dayhoff, M.O., ed., Atlas of Protein Sequence and Structures, Vol. 5, Suppl. 3, 345-58, National Biomedical Research Foundation, Washington, D.C.
7. Dayhoff, M.O., Barker, W.C., and Hunt, L.T. 1983. Establishing homologies in protein sequences. Methods Enzym 91, 524-545.
8. Fields, C.A., and Soderlund, C.A. 1990. Gm: a practical tool for automating DNA sequence analysis. Comput. Appl. Biol. Sci. 6, 263-270.
9. Gelfand, M.S. 1992. Statistical analysis and prediction of the exonic structure of human genes. J. Mol. Evol. 35, 239-252.
10. Gelfand, M.S., Mironov, A.A., and Pevzner, P.A. 1996. Gene recognition via spliced sequence alignment. Proc. Natl. Acad. Sci. USA, 93, 9061-9066.
11. Green, P., Lipman, D., Hillier, L., Waterston, R., States, D., and Claverie, J.-M. 1993. Ancient conserved regions in new gene sequences and the protein databases. Science 259, 1711-1716.
12. Guigo, R., Knudsen, S., Drake, N., and Smith, T. 1992. Prediction of gene structure. J. Mol. Biol. 226, 141-157.
13. Henikoff, S., and Henikoff, J.G. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA, 89, 10915-10919.
14. Jorgensen, J., Buskirk, S.F., Gribskov, M., and Smith, D.W. 1995. SEARCH: Locating and identifying genes in large genomic sequences using parallel computers, 143-158. In Lim, H.A., and Cantor, C.R., eds., Proceedings of the Third International Conference on Bioinformatics and Genome Research, World Scientific Publishing Co., Ltd., Singapore.
15. Karlin, S., and Altschul, S.F. 1990. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. USA 87, 2264-2268.
16. Seely, O., Jr., Feng, D.-F., Smith, D.W., Sulzbach, D., and Doolittle, R.F. 1990. Construction of a facsimile data set for large genome sequence analysis. Genomics 8, 71-82.
17. Smith, D.W., Jorgensen, J., Greenberg, J.P., Keller, J., Rogers, J., Garner, H.R., and Ten Eyck, L. 1993. Supercomputers, parallel processing, and genome projects, 51-86. In Smith, D.W., ed., Biocomputing: Informatics and Genome Projects, Academic Press, San Diego, CA.
18. Smith, M.W. 1988. Structure of vertebrate genes: a statistical analysis implicating selection. J. Mol. Evol. 27, 45-55.
19. Snyder, E.E., and Stormo, G.D. 1993. Identifying genes in genomic DNA sequences: An application of dynamic programming and neural networks. Nucl. Acids Res. 21, 607-613.
20. Uberbacher, E.C., and Mural, R.J. 1991. Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach. Proc. Natl. Acad. Sci. U.S.A. 88, 11261-11265.
21. Wootton, J.C., and Federhen, S. 1993. Statistics of local complexity in amino acid sequences and sequence databases. Computers Chem. 17, 149-163.
22. Xu, Y., Mural, R., Shah, M., and Uberbacher, E. 1994a. Recognizing exons in genomic sequence using GRAIL II. Genetic Engineering 16, 241-253.
23. Xu, Y., Mural, R.J., and Uberbacher, E.C. 1994b. Constructing gene models from accurately predicted exons: An application of dynamic programming. Comput. Appl. Biol. Sci. 10, 613-623.