Orphan gene finding—an exon assembly approach

Theoretical Computer Science

Volumn 290, Issue 3, 2003, Pages 1407-1431

  Blayo, Philippe ^a   Rouzé, Pierre ^b   Sagot, Marie France ^c  

^a Université de Marne la Vallée   (France)

^b GHENT UNIVERSITY   (Belgium)

^c UNIVERSITÉ LYON 1   (France)

Author keywords

Coding DNA comparison models; DNA DNA and DNA protein comparison; Dynamic programming; Exon assembly; Gene finding; Orphan gene

Indexed keywords

BIOINFORMATICS; CODES (SYMBOLS); DNA; DNA SEQUENCES; DYNAMIC PROGRAMMING;

ASSEMBLY APPROACH; COMPARISON MODELS; EUKARYOTIC GENES; GENE FAMILIES; GENE FINDING; SEQUENCE COMPARISONS; SPACE COMPLEXITY; TIME COMPLEXITY;

GENES;

EID: 85009205020     PISSN: 03043975     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0304-3975(02)00043-9     Document Type: Article

References (36)

1. [1] Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J., Basic local alignment search tool. J. Mol. Biol. 215 (1990), 403–410.
2. [2] Arvestad, L., Aligning coding DNA in the presence of frameshift errors. Farach-Colton, M., (eds.) Combinatorial Pattern Matching, 1997, Lecture Notes in Computer Science, Vol. 1264, 1997, Springer, Berlin, 180–190.
3. [3] Bafna, V., Huson, D.H., The conserved exon method for gene finding. Bourne, P., Gribskov, M., Altman, R., Jensen, N., T. Lengauer, D.Hope, Mitchell, J., Scheeff, E., Smith, C., Strande, S., Weissig, (eds.) 8th Internat. Conf. on Intelligent Systems for Molecular Biology, 2000, AAAI Press, San Diego, California, USA.
4. [4] Batzoglou, S., Pachter, L., Mesirov, J.P., Berger, B., Lander, E.S., Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Res. 10 (2000), 950–958.
5. [5] C. Burge, Identification of genes in human genomic DNA, Ph.D. Thesis, Stanford University, Stanford, CA, USA, 1997.
6. [6] Burge, C., Karlin, S., Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268 (1997), 78–94.
7. [7] Burset, M., Guigó, R., Evaluation of gene structure prediction programs. Genomics 34 (1996), 353–367.
8. [8] Claverie, J.-M., Computational methods for the identification of genes in vertebrate genomic sequence. Hum. Mol. Genet. 6 (1997), 1735–1744.
9. [9] Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C., A model of evolutionary change in proteins. Atlas of Protein Sequence and Structure (Natl. Biomed. Res. Found.) 5:suppl. 3 (1978), 345–352.
10. [10] Dujon, B., The yeast genome project: what did we learn?. Trends Genet. 12 (1996), 263–270.
11. [11] Durbin, R., Eddy, S.R., Krogh, A., Mitchison, G., Biological Sequence Analysis, Probabilistic Models of Proteins and Nucleic Acids, 1998, Cambridge University Press, Cambridge.
12. [12] Fickett, J.W., Recognition of protein coding regions in DNA sequences. Nucleic Acids Res. 10 (1982), 5503–5518.
13. [13] Ficket, J.W., Finding genes by computer: the state of the art. Trends Genet. 12 (1996), 316–320.
14. [14] Florea, L., Hartzell, G., Zhang, Z., Rubin, G.M., Miller, W.M., A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 8 (1998), 967–974.
15. [15] Gelfand, M.S., Computer prediction of the exon–intron structure of mammalian pre-mRNAs. Nucleic Acids Res. 18 (1990), 5865–5869.
16. [16] Gelfand, M.S., Mironov, A., Pevzner, P.A., Spliced alignment problem: a new approach to gene recognition. Hirschberg, D.S., Myers, E.W., (eds.) Combinatorial Pattern Matching, Lecture Notes in Computer Science, Vol. 1075, 1996, Springer, Berlin, 141–158.
17. [17] Gelfand, M.S., Mironov, A.A., Pevzner, P.A., Gene recognition via spliced sequence alignment. Proc. Natl. Acad. Sci. (USA) 93 (1996), 9061–9066.
18. [18] Gotoh, O., An improved algorithm for matching biological sequences. J. Mol. Biol. 162 (1982), 705–708.
19. [19] Guan, X., Uberbacher, E.C., Alignments of DNA and protein sequences containing frameshift errors. Comp. Appl. Biol. Sci. 12:1 (1996), 31–40.
20. [20] Guigó, R., Assembling genes from predicted exons in linear time with dynamic programming. J. Comput. Biol. 5:4 (1998), 681–702.
21. [21] Hein, J., An algorithm combining DNA and protein alignment. J. Theoret. Biol. 167 (1994), 169–174.
22. [22] Hein, J., Stovlbaek, J., Combined DNA and protein alignment. Methods Enzymol. 266 (1996), 402–418.
23. [23] Henikoff, S., Henikoff, J.G., Amino acid substitution matrices for protein blocks. Proc. Natl. Acad. Sci. USA 89 (1992), 10915–10919.
24. [24] Hirschberg, D.S., A linear space algorithm for computing maximal common subsequences. ACM 18 (1975), 341–343.
25. [25] Hua, Y., Jiang, T., Wu, B., Aligning DNA sequences to minimize change in protein. Farach-Colton, M., (eds.) Combinatorial Pattern Matching, 1998, Lecture Notes in Computer Science, Vol. 1448, 1998, Springer, Berlin, 221–234.
26. [26] Hutchinson, G.B., Hayden, M.R., The prediction of exons through an analysis of spliceable open reading frames. Nucleic Acids Res. 20 (1992), 3453–3462.
27. [27] Myers, E.W., Miller, W., Optimal alignments in linear space. Comput. Appl. Biosci. 4 (1988), 11–17.
28. [28] N. Pavy, S. Rombauts, P. Déhais, C. Mathé, D.V.V. Ramana, P. Leroy, P. Rouzé, Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences, BioInformatics 15 (1999) 887–899.
29. [29] C.N.S. Pedersen, personal communication.
30. [30] Pedersen, C.N.S., Lyngso, R., Hein, J., Comparison of coding DNA. Farach-Colton, M., (eds.) Combinatorial Pattern Matching, 1998, Lecture Notes in Computer Science, Vol. 1448, 1998, Springer, Berlin, 153–173.
31. [31] Shepherd, J.C.W., Method to determine the reading frame of a protein from the purine/pyrimidine genome sequence and its possible evolutionary justification. Proc. Natl. Acad. Sci. 78 (1981), 1576–1600.
32. [32] Staden, R., McLachlan, A.D., Codon preference and its use in identifying protein coding regions in long DNA sequences. Nucleic Acids Res. 10 (1982), 5503–5518.
33. [33] Terryn, N., Heijnen, L., De Keyser, A., Van Asseldonck, M., De Clercq, R., Verbakel, H., Gielen, J., Zabeau, M., Villarroel, R., Jesse, T., Neyt, P., Hogers, R., Van Den Daele, H., Ardiles, W., Schueller, C., Mayer, K., Déhais, P., Rombauts, S., Van Montagu, M., Rouz,. Vos, P., Evidence for an ancient chromosomal duplication in Arabidopsis thaliana by sequencing and analyzing a 400-kb contig at the APETALA2 locus on chromosome 4. FEBS Lett. 445 (1999), 237–245.
34. [34] Thomas, A., Skolnick, M.H., A probabilistic model for detecting coding regions in DNA sequences. IMA J. Math. Appl. Med. Biol. 11 (1994), 149–160.
35. [35] Wiehe, T., Gebauer-Jung, S., Mitchell-Olds, T., Guigo, R., SGP-1: prediction and validation of homologous genes based on sequence alignments. Genome Res. 11 (2001), 1574–1583.
36. [36] Y. Xu, J.R. Einstein, R.J. Mural, M. Shah, E.C. Uberbacher, An improved system for exon recognition and gene modeling in human DNA sequences, 2nd Internat. Conf. on Intelligent Systems for Molecular Biology, AAAAI Press, Menlo Park, California, 1994, pp. 376–384.