Optimal spliced alignment of homologous cDNA to a genomic DNA template

Bioinformatics

Volumn 16, Issue 3, 2000, Pages 203-211

  Usuka, Jonathan ^a   Zhu, Wei ^b   Brendel, Volker ^b  

^a STANFORD UNIVERSITY   (United States)

^b IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

ALGORITHM; ARTICLE; COMPUTER PROGRAM; DNA TEMPLATE; EXPRESSED SEQUENCE TAG; GENE LOCUS; GENOME; INTERNET; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; RNA SPLICING; SEQUENCE HOMOLOGY;

EID: 0034129194     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/16.3.203     Document Type: Article

References (19)

1. Altschul, S.F., Madden, T.L., Schaffer, 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.
2. Birney, E., Thompson, J.D. and Gibson, T.J. (1996) Pair-wise and searchwise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames. Nucl. Acids Res., 24, 2730-2739.
3. Brendel, V. and Kleffe, J. (1998) Prediction of locally optimal splicesites in plant pre-mRNA with applications to gene identification in Arabidopsis thaliana genomic DNA. Nucl. Acids Res., 26, 4748-4757.
4. Brendel, V., Carle-Urioste, J.C. and Walbot, V. (1998) Intron recognition in plants. In Bailey-Serres, J. and Gallie, D.R. (eds), A Look Beyond Transcription: Mechanisms Determining mRNA Stability and Translation in Plants American Society of Plant Physiology, Rockville, MD, pp. 20-28.
5. Burge, C. and Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78-94.
6. Claverie, J.-M. (1997) Computational methods for the identification of genes in vertebrate genomic sequences. Hum. Mol. Genet., 6, 1735-1744.
7. 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.
8. 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.
9. Gotoh, O. (1982) An improved algorithm for matching biological sequences. J. Mol. Biol., 162, 705-708.
10. Hebsgaard, S.M., Korning, P.G., Tolstrup, N., Engelbrecht, J., Rouzé, P. and Brunak, S. (1996) Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. Nucl. Acids Res., 24, 3439-3452.
11. Henikoff, S. and Henikoff, J.G. (1992) Amino acid substitution matrices fromprotein blocks. Proc. Natl. Acad. Sci. USA, 89, 10915-10919.
12. Huang, X. (1994) On global sequence alignment. Comput. Appl. Biosci., 10, 227-235.
13. Huang, X. and Zhang, J. (1996) Methods for comparing a DNA sequence with a protein sequence. Comput. Appl. Biosci., 12, 497-506.
14. Huang, X., Adams, M.D., Zhou, H. and Kerlavage, A.R. (1997) A tool for analyzing and annotating genomic sequences. Genomics, 46, 37-45.
15. Karlin, S., Weinstock, G. and Brendel, V. (1995) Bacterial classifications derived from RecA protein sequence comparisons. J. Bacteriol., 6881-6893.
16. Kleffe, J., Hermann, K., Vahrson, W., Wittig, B. and Brendel, V. (1996) Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences. Nucl. Acids Res., 24, 4709-4718.
17. Manber, U. and Myers, G. (1993) Suffix arrays: a new method for on-line search. SIAM J. Comput., 22, 935-948.
18. Mott, R. (1997) EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA. Comput. Appl. Biosci., 13, 477-478.
19. Usuka, J. and Brendel, V. (2000) Gene structure prediction by spliced alignment of genomic DNA with protein sequences: increased accuracy by differential splice site scoring. J. Mol. Biol., 297, 1075-1085.