A dictionary-based approach for gene annotation

Journal of Computational Biology

Volumn 6, Issue 3-4, 1999, Pages 419-430

  Pachter, Lior ^a   Batzoglou, Serafim ^a   Spitkovsky, Valentin I ^a   Banks, Eric ^a   Lander, Eric S ^b   Kleitman, Daniel J ^a   Berger, Bonnie ^a,c  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Alternative splicing; Exon prediction; Gene recognition; Splice site detection

Indexed keywords

ALTERNATIVE RNA SPLICING; CONFERENCE PAPER; DNA SEQUENCE; EXON; GENE EXPRESSION; GENE LOCUS; GENE STRUCTURE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE HOMOLOGY;

ALTERNATIVE SPLICING; ANIMALS; DATABASES, FACTUAL; DICTIONARIES; EXONS; EXPRESSED SEQUENCE TAGS; GENES; GENETIC TECHNIQUES; HUMANS; PROTEINS; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 0032743426     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/106652799318364     Document Type: Conference Paper

References (26)

1. RepeatMasker. http://ftp.genome.washington.edu/cgi-bin/RepeatMasker, 1998.
2. dbEST. http://www.ncbi.nlm.nih.gov/dbEST/index.html, 1998.
3. OWL. http://bmbsgi11.leeds.ac.uk/bmb5dp/owl.html, 1998.
4. Altschul, S.F., Gish, S.F., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. Journal of Molecular Biology, 215, 403-410.
5. 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. Nucleic Acids Res. 25, 3389-3402.
6. Batzoglou, S., Berger, B., Kleitman, D.J., Lander, E.S., and Pachter, L. 1998. Recent developments in computational gene recognition. Doc. Math. Extra Volume ICM 1998 1, 649-658.
7. Benson, G. 1997. Sequence alignment with tandem duplication. J. Comp. Biol. 4(3), 351-367.
8. Burge, C., and Karlin, S. 1997. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78-94.
9. Burset, M., and Guigó, R. 1996. Evaluation of gene structure prediction programs. Genomics 34(3), 353-367.
10. Deed, R.W., Jasiok, M., and Norton, J.D. 1996. Attenuated function of a variant form of the helix-loop-helix protein, Id-3, generated by an alternative splicing mechanism. FEBS Lett. 393, 113-116.
11. Gelfand, M.S., Mironov, A.A., and Pevzner, P.A. 1996. Gene recognition via spliced sequence alignment. Proc. Natl. Acad. Sci. U.S.A. 93, 9061-9066.
12. Guigó, R. 1997. Computational gene identification: An open problem. Comput. Cliem. 21(4), 215-222.
13. Haussler, D., Kulp, D., and Reese, M. 1996. A representative benchmark gene data set. http://www-hgc.lbl. gov/inf/genesets.html.
14. Henderson, J., Salzberg, S., and Fasman, K.H. 1997. Finding genes in DNA with a hidden Markov model. J. Comp. Biol. 4(2), 127-141.
15. Huang, X., Adams, M.D., Zhou, H., and Kerlavage, A. 1997. A tool for analyzing and annotating genomic sequences. Genomics 46, 37-45.
16. Kozak, M. 1981. Possible role of flanking nucleotides in recognition of the AUG initiator codon by eukaryotic ribosomes. Nucleic Acids Res. 9, 5233-5252.
17. Kulp, D., Haussler, D., Reese, M.G., and Eeckman, F.H. 1996. A generalized hidden Markov model for the recognition of human genes in DNA. Proc. 4th Conf. Intelligent Syst. Mol. Biol., 134-142.
18. Laub, M., and Smith, D.W. 1998. Finding intron/exon splice junctions using INFO, INterruption finder and organizer. J. Comp. Biol. 5(2), 307-321.
19. Lukashin, A.V., and Borodovsky, M. 1998. GENEMARK.HMM: New solutions for gene finding. Nucleic Acids Res. 26(4), 1107-1115.
20. Mironov, A., Roytberg, M.A., Pevzner, P.A., and Gelfand, M.S. 1998. Performance-guarantee gene predictions via spliced alignment. Genomics 51, 332-339.
21. Rigoutsos, I., and Califano, A. 1994. Searching in parallel for similar strings. Computational Science and Engineering 1(2), 60-75.
22. Solovyev, V.V., Salamov, A.A., and Lawrence, C.B. 1995. Identfication of human gene structure using linear discriminant functions and dynamic programming. Proc. 3rd Conf. Intelligent Syst. Mol. Bio., pages 367-375.
23. Sze, S., and Pevzner, P.A. 1997. Las Vegas algorithms for gene recognition: Suboptimal and error-tolerant spliced alignment. J. Comp. Biol. 4(3), 297-309.
24. Waterman, M.S. 1998. Introduction to Computational Biology: Maps, Sequences and Genomes. Chapman & Hall.
25. Xu, Y., Mural, R.J., Shah, M., and Uberbacher, E.C. 1994. Recognizing exons in genomic sequences using GRAIL II. In Setlow, J., ed., Genetic Engineering: Principles and Methods, Volume 16. Plenum Press, New York.
26. Zhang, Z., Pearson, W.R. and Miller, W. 1997. Aligning a DNA sequence with a protein sequence. J. Comp. Biol. 4(3), 339-349.