Performance-guarantee gene predictions via spliced alignment

Genomics

Volumn 51, Issue 3, 1998, Pages 332-339

  Mironov, Andrey A ^a   Roytberg, Michael A ^b   Pevzner, Pavel A ^d   Gelfand, Mikhail S ^c  

^a Natl Ctr for Biotech NIIGENETIKA   (Russian Federation)

^b INSTITUTE OF MATHEMATICAL PROBLEMS OF BIOLOGY   (Russian Federation)

^c INSTITUTE OF PROTEIN RESEARCH   (Russian Federation)

^d UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CORRELATION FUNCTION; DNA SEQUENCE; GENE MAPPING; GENE SEQUENCE; GENOME; HUMAN; NONHUMAN; PRIORITY JOURNAL; RNA SPLICING;

PROKARYOTA;

EID: 0032143413     PISSN: 08887543     EISSN: None     Source Type: Journal    
DOI: 10.1006/geno.1998.5251     Document Type: Article

References (19)

1. Altschul S. F. Amino acid substitution matrices from an information theoretic perspective. J. Mol. Biol. 219:1991;555-565.
2. Benson D. A., Boguski M. S., Lipman D. J., Ostell J. GenBank. Nucleic Acids Res. 25:1997;1-6.
3. Burset M., Guigo R. Evaluation of gene structure prediction programs. Genomics. 34:1996;353-367.
4. Fickett J. W. The gene identification problem: An overview for developers. Comput. Chem. 20:1996a;103-118.
5. Fickett J. W. Finding genes by computer: The state of the art. Trends Genet. 12:1996b;316-320.
6. Gelfand M. S. Prediction of function in DNA sequence analysis. J. Comput. Biol. 2:1995;87-115.
7. Gelfand M. S., Mironov A. A., Pevzner P. A. Gene recognition via spliced sequence alignment. Proc. Natl. Acad. Sci. USA. 93:1996a;9061-9066.
8. Gelfand M. S., Podolsky L. I., Astakhova T. V., Roytberg M. A. Recognition of gene in human DNA sequences. J. Comput. Biol. 3:1996b;223-234.
9. Gish W., States D. J. Identification of protein coding regions by database similarity search. Nat. Genet. 3:1993;266-272.
10. Hultner M., Smith D. W., Wills C. Similarity landscapes: A way to detect many structural and sequence motifs in both introns and exons. J. Mol. Evol. 38:1994;188-203.
11. Jackson I. J. A reappraisal of non-consensus mRNA splice sites. Nucleic Acids Res. 19:1991;3795-3798.
12. Rogozin I. B., Milanesi L., Kolchanov N. A. Gene structure prediction using information on homologous protein sequence. Comput. Appl. Biosci. 12:1996;161-170.
13. Schuler G. D., Epstein J. A., Ohkawa H., Kans J. A. Entrez: Methods Enzymol. 266:1996;141-162.
14. Sharp P. A. Split genes and RNA splicing. Cell. 77:1994;805-815.
15. Snyder E. E., Stormo G. D. Identification of protein coding regions in genomic DNA. J. Mol. Biol. 248:1995;1-18.
16. Stoesser G., Sterk P., Tuli M. A., Stoehr P., Cameron G. N. The EMBL nucleotide sequence database. Nucleic Acids Res. 25:1997;7-13.
17. Sze S.-H., Pevzner P. A. Las Vegas algorithms for gene recognition: Subotimal and error tolerant spliced alignment. J. Comput. Biol. 4:1997;297-310.
18. Uberbacher E. C., Mural R. J. Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach. Proc. Natl. Acad. Sci. USA. 88:1991;11261-11265.
19. Uberbacher E. D., Xu Y., Mural R. J. Discovering and understanding genes in human DNA sequence using GRAIL. Methods Enzymol. 266:1996;259-281.