A tool for analyzing and annotating genomic sequences

Genomics

Volumn 46, Issue 1, 1997, Pages 37-45

  Huang, Xiaoqiu ^a   Adams, Mark D ^b   Zhou, Hao ^a   Kerlavage, Anthony R ^b  

^a Michigan Technological University   (United States)

^b J CRAIG VENTER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; ARTICLE; BASE PAIRING; DATA BASE; DIAGNOSTIC TEST; DNA DETERMINATION; DNA SEQUENCE; EXON; GENE SEQUENCE; GENETIC ANALYSIS; INTRON; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA INTERACTION;

ANIMALIA;

EID: 0031573382     PISSN: 08887543     EISSN: None     Source Type: Journal    
DOI: 10.1006/geno.1997.4984     Document Type: Article

References (19)

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. Burge, C., and Karlin, S. (1997). Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268: 78-94.
3. Burset, M., and Guigo, R. (1996). Evaluation of gene structure prediction programs. Genomics 34: 353-367.
4. Chao, K-M., Zhang, J., Ostell, J., and Miller, W. (1995). A local alignment tool for very long DNA sequences. Comput. Appl. Biosci. 11: 147-153.
5. Fickett, J. W. (1996). The gene identification problem: An overview for developers. Comput. Chem. 20: 103-118.
6. 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.
7. Gish, W., and States, D. J. (1993). Identification of protein coding regions by database similarity search. Nature Genet. 3: 266-272.
8. Guan, X., and Uberbacher, E. C. (1996). Alignments of DNA and protein sequences containing frameshift errors. Comput. Appl. Biosci. 12: 31-40.
9. Huang, X. (1992). A contig assembly program based on sensitive detection of fragment overlaps. Genomics 14: 18-25.
10. Huang, X. (1994). On global sequence alignment. Comput. Appl. Biosci. 10: 227-235.
11. Huang, X. (1996). Fast comparison of a DNA sequence with a protein sequence database. Microb. Comp. Genomics 1: 281-291.
12. Huang, X., and Miller, W. (1991). A time-efficient, linear-space local similarity algorithm. Adv. Appl. Math. 12: 337-357.
13. Huang, X., and Zhang, J. (1996). Methods for comparing a DNA sequence with a protein sequence. Comput. Appl. Biosci. 12: 497-506.
14. Kulp, D., Reese, M. G., Eeckman, F. H., and Haussler, D. (1997). Integrating database homology in a probabilistic gene structure model. "Pacific Symposium on Biocomputing," World Scientific Press, New York.
15. Snyder, E. E., and Stormo, G. D. (1995). Identification of protein coding regions in genomic DNA. J. Mol. Biol. 248: 1-18.
16. Staden, R. (1984). Computer methods to locate signals in nucleic acid sequences. Nucleic Acids Res. 12: 505-519.
17. Xu, Y., Mural, R. J., Shah, M., and Uberbacher, E. C. (1994). Recognizing exons in genomic sequence using GRAIL II. In "Genetic Engineering: Principles and Methods" (J. Setlow, Ed.), pp. 241-253, Plenum, New York.
18. Zhang, J. (1996). PowerBLAST: A new network BLAST application for genomic sequence analysis. "Genome Mapping and Sequencing," p. 19. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
19. Zhang, Z., Pearson, W., and Miller, W. (1997). Aligning a DNA sequence with a protein sequence. In "Proceedings of the First Annual International Conference on Computational Molecular Biology," pp. 337-343, Santa Fe, NM.