Homology-based gene structure prediction: Simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps

Bioinformatics

Volumn 16, Issue 3, 2000, Pages 190-202

  Gotoh, Osamu ^a  

^a SAITAMA CANCER CENTER   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CAENORHABDITIS ELEGANS; COMPUTER PROGRAM; CORRELATION FUNCTION; DNA SEQUENCE; FRAMESHIFT MUTATION; GENE FUNCTION; GENETIC CODE; INTERNET; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROTEIN EXPRESSION; RNA SPLICING; SEQUENCE HOMOLOGY; STOP CODON; TRANSLATION INITIATION;

EID: 0034129662     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/16.3.190     Document Type: Article

References (47)

1. 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.
2. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res., 25, 3389-3402.
3. Birney, E. and Durbin, R. (1997) Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison. ISMB, 5, 56-64.
4. Burge, C. and Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78-94.
5. Burge, C.B. and Karlin, S. (1998) Finding the genes in genomic DNA. Curr. Opin. Struct. Biol., 8, 346-354.
6. Burset, M. and Guigó, R. (1996) Evaluation of gene structure prediction programs. Genomics, 34, 353-367.
7. Cai, Y. and Bork, P. (1998) Homology-based gene prediction using neural nets. Anal. Biochem., 265, 269-274.
8. Chao, K.-M. (1999) Calign: aligning sequences with restricted affine gap penalties. Bioinformatics, 15, 298-304.
9. Claverie, J.-M. (1997) Computational methods for the identification of genes in vertebrate genomic sequences. Hum. Mol. Genet., 6, 1735-1744.
10. Crick, F.H.C. (1968) The origin of the genetic code. J. Mol. Biol., 38, 367-379.
11. Dayhoff, M.O., Schwartz, R.M. and Orcutt, B.C. (1978) A model of evolutionary change in proteins. In Dayhoff, M.O. (ed.), Atlas of Protein Sequence and Structure. Vol. 5, Suppl. 3, National Biomedical Research Foundation, Washington, D.C., pp. 345-352.
12. Doolittle, R.F. (1981) Similar amino acid sequences: chance or common ancestry?. Science, 214, 149-159.
13. Fickett, J.W. and Tung, C.-S. (1992) Assessment of protein coding measures. Nucl. Acids Res., 20, 6441-6450.
14. Florea, L., Hartzell, G., Zhang, Z., Rubin, G.M. and Miller, W. (1998) A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res., 8, 967-974.
15. 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.
16. Goffeau, A., Barrell, B.G., Bussey, H., Davis, R.W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J.D., Jacq, C., Johnston, M., Louis, E.J., Mewes, H.W., Murakami, Y., Philippsen, P., Tettelin, H. and Oliver, S.G. (1996) Life with 6000 genes. Science, 274, 546-567.
17. Gotoh, O. (1990) Optimal sequence alignment allowing for long gaps. Bull. Math. Biol., 52, 359-373.
18. Gotoh, O. (1993) Optimal alignment between groups of sequences and its application to multiple sequence alignment. Comput. Appl. Biosci., 9, 361-370.
19. Gotoh, O. (1994) Further improvement in methods of group-to-group sequence alignment with generalized profile operations. Comput. Applic. Biosci., 10, 379-387.
20. Gotoh, O. (1995) A weighting system and algorithm for aligning many phylogenetically related sequences. Comput. Applic. Biosci., 11, 543-551.
21. Gotoh, O. (1996) Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J. Mol. Biol., 264, 823-838.
22. Gotoh, O. (1998) Divergent structures of Caenorhabditis elegans cytochrome P450 genes suggest the frequent loss and gain of introns during the evolution of nematodes. Mol. Biol. Evol., 15, 1447-1459.
23. Gribskov, M., McLachlan, A.D. and Eisenberg, D. (1987) Profile analysis: detection of distantly related proteins. Proc. Natl Acad. Sci. USA, 84, 4355-4358.
24. Guigó, R. and Fickett, J.W. (1995) Distinctive sequence features in protein coding genic non-coding, and intergenic human DNA. J. Mol. Biol., 253, 51-60.
25. Hein, J. (1994) An algorithm combining DNA and protein alignment. J. Theor. Biol., 167, 169-174.
26. Huang, X. and Zhang, J. (1996) Methods for comparing a DNA sequence with a protein sequence. Comput. Applic. Biosci., 12, 497-506.
27. Jansen, G., Thijssen, K.L., Werner, P., van der Horst, M., Hazendonk, E. and Plasterk, R.H.A. (1999) The complete family of genes encoding G proteins of Caenorhabditis elegans. Nature Genet., 21, 414-419.
28. Jones, D.T., Taylor, W.R. and Thornton, J.M. (1992) The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci., 8, 275-282.
29. Lolkema, J.S. and Slotboom, D.-J. (1998) Hydropathy profile alignment: a tool to search for structural homologues of membrane proteins. FEMS Microbiol. Rev., 22, 305-322.
30. Mironov, A.A., Roytberg, M.A., Pevzner, P.A. and Gelfand, M.S. (1998) Performance-guarantee gene predictions via spliced alignment. Genomics, 51, 332-339.
31. Mott, R. (1997) EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA. Comput. Appl. Biosci., 13, 477-478.
32. Murakami, K. and Takagi, T. (1998) Gene recognition by combination of several gene-finding programs. Bioinformatics, 14, 665-675.
33. Myers, E.W. and Miller, W. (1988) Optimal alignments in linear space. Comput. Appl. Biosci., 4, 11-17.
34. Park, J., Karplus, K., Barrett, C., Hughey, R., Haussler, D., Hubbard, T. and Chothia, C. (1998) Sequence comparison using multiple sequences detect three times as many remote homologues as pairwise methods. J. Mol. Biol., 284, 1201-1210.
35. Pearson, W.R., Wood, T., Zhang, Z. and Miller, W. (1997) Comparison of DNA sequences with protein sequences. Genomics, 46, 24-36.
36. Peltola, H., Söderlund, H. and Ukkonen, E. (1986) Algorithms for the search of amino acid patterns in nucleic acid sequences. Nucl. Acids Res., 14, 99-107.
37. Salzberg, S.L. (1997) A method for identifying splice sites and translational start sites in eukaryotic mRNA. Comput. Applic. Biosci., 13, 365-376.
38. Sander, C. and Schneider, R. (1991) Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins, 9, 56-68.
39. Sankoff, D. and Kruskal, J.B. (1983) Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison. Addison-Wesley, New York.
40. Sellers, P.H. (1979) Pattern recognition in genetic sequences. Proc. Natl Acad. Sci. USA, 76, 3041.
41. Snyder, E.E. and Stormo, G.D. (1995) Identification of protein coding regions in genomic DNA. J. Mol. Biol., 248, 1-18.
42. Sonnhammer, E.L.L. and Durbin, R. (1997) Analysis of protein domain families in Caenorhabditis elegans. Genomics, 46, 200-216.
43. The C. elegans Sequencing Consortium (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science, 282, 2012-2018.
44. 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. USA, 88, 11261-11265.
45. Xu, Y., Mural, R.J. and Uberbacher, E.C. (1994) Constructing gene models from accurately predicted exons: an application of dynamic programming. Comput. Appl. Biosci., 10, 613-623.
46. Zhang, M.Q. (1997) Identification of protein coding regions in the human genome by quadratic discriminant analysis. Proc. Natl Acad. Sci. USA, 94, 565-568.
47. Zhang, M.Q. and Marr, T.G. (1993) A weight array method for splicing signal analysis. Comput. Applic. Biosci., 9, 499-509.