Comparison of DNA sequences with protein sequences

Genomics

Volumn 46, Issue 1, 1997, Pages 24-36

  Pearson, William R ^a   Wood, Todd ^a   Zhang, Zheng ^b   Miller, Webb ^b  

^a UNIVERSITY OF VIRGINIA   (United States)

^b The Pennsylvania State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ANIMAL CELL; ARTICLE; CODON; COMPARATIVE STUDY; DNA PROTEIN COMPLEX; DNA SEQUENCE; FRAMESHIFT MUTATION; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; RNA TRANSLATION; SEQUENCE HOMOLOGY; TRANSLATION REGULATION;

ANIMALIA; HAEMOPHILUS INFLUENZAE; METHANOCALDOCOCCUS JANNASCHII; METHANOCOCCUS; MYCOPLASMA GENITALIUM; MYCOPLASMATALES;

EID: 0031573415     PISSN: 08887543     EISSN: None     Source Type: Journal    
DOI: 10.1006/geno.1997.4995     Document Type: Article

References (22)

1. Bult, C. J., White, O., Olsen, G. J., Zhou, L., Fleischmann, R. D., Sulton, G. G., Blake, J. A., Fitzgerald, L. M., Clayton, R. A., Gocayne, J. D., Kerlavage, A. R., Dougherty, B. A., Tomb, J.-F., Adams, M. D., Reisch, C. I., Overbeek, R., Kirkness, E. F., Weinstock, K. G., Merrick, J. M., Glodek, A., Scott, J. L., Geoghagen, N. S. M., Weidman, J. F., Fuhrmann, J. L., Nguyen, D., Utterback, T. R., Kelley, J. M., Peterson, J. D., Sadow, P. W., Hanna, M. C., Cotton, M. D., Roberts, K. M., Hurst, M. A., Kaine, B. P., Borodovsky, M., Klenk, H.-P., Fraser, C. M., Smith, H. O., Woese, C. R., and Venter, J. C. (1996). Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273: 1058-1073.
2. Chao, K.-M., Pearson, W. R., and Miller, W. (1992). Aligning two sequences within a specified diagonal band. Comp. Appl. Biosci. 8: 481-487.
3. Fleischmann, R. D., Adams, M. D., White, O., Clayton, R. A., Kirkness, E. F., Kerlavage, A. R., Bult, C. J., Tomb, J. F., Dougherty, B. A., Merrick, J. M., McKenney, K., Sutton, G., FitzHugh, W., Fields, C., Gocayne, J. D., Scott, J., Shirley, R., Liu, L.-I., Glodek, A., Kelley, J. M., Weidman, J. F., Phillips, C. A., Spriggs, T., amd M. D. Cotton, E. H., Utterback, T. R., Hanna, M. C., Nguyen, D. T., Saudek, D. M., Brandon, R. C., Fine, L. D., Fritchman, J. L., Fuhrmann, J. L., Geoghagen, N. S. M., Gnehm, C. L., McDonald, L. A., Small, K. V., Fraser, C. M., Smith, H. O., and Venter, J. C. (1995). Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496-512.
4. Fraser, C. M., Gocayne, J. D., White, O., Adams, M. D., Clayton, R. A., Fleischmann, R. D., Bult, C. J., Kerlavage, A. R., Sutton, G., Kelley, J. M., Fritchman, J. L., Weidman, J. F., Small, K. V., Sandusky, M., Fuhrmann, J., Nguyen, D., Utterback, T. R., Saudek, D. M., Phillips, C. A., Merrick, J. M., Tomb, J.-F., Dougherty, B. A., Bott, K. F., Hu, P.-C., Lucier, T. S., Peterson, S. N., Smith, H. O., III, C. A. H., and Venter, J. C. (1995). The minimal gene complement of Mycoplasma genitalium. Science 270: 397-403.
5. Gish, W., and States, D. J. (1993). Identification of protein coding regions by database similarity search. Nature Genet. 3: 266-272.
6. Guan, X., and Uberbacher, E. (1996). Alignments of DNA and protein sequences containing frameshift errors. Comp. Appl. Biosci. 12: 31-40.
7. Hein, J. (1994). An algorithm combining DNA and protein alignment. J. Theor. Biol. 167: 169-174.
8. Hein, J., and Stovbaek, J. (1994). Genomic alignment. J. Mol. Evol. 38: 310-316.
9. Henikoff, S., and Henikoff, J. G. (1992). Amino acid substitutions matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89: 10915-10919.
10. Hillier, L., Lennon, G., Becker, M., Bonaldo, M. F., Chiapelli, B., Chissoe, S., Dietrich, N., DuBuque, T., Favello, A., Gish, W., Hawkins, M., Hultman, M., Kucaba, T., Lacy, M., Le, M., Le, N., Mardis, E., Moore, B., Morris, M., Parsons, J., Prange, C., Rifkin, L., Rohlfing, T., Schellenberg, K., Soares, M. B., Tan, F., Thierry-Meg, J., Trevaskis, E., Underwood, K., Wohldman, P., Waterston, R., Wilson, R., and Marra, M. (1996). Generation and analysis of 280,000 human expressed sequence tags. Genome Res. 6: 807-828.
11. Huang, X., and Zhang, J. (1996). Methods for comparing a DNA sequence with a protein sequence. Comp. Appl. Biosci. 12: 497-506.
12. Knecht, L. (1995). Pairwise alignment with scoring on tuples. In "Lecture Notes in Computer Science: Combinatorial Pattern Matching," Vol. 937, pp. 215-229, Springer-Verlag, Berlin.
13. Koonin, E. V., Mushegian, A. R., Tatusov, R. L., Altschul, S. F., Bryant, S. H., Bork, P., and Valencia, A. (1994). Eukaryotic translation elongation factor 1 gamma contains a glutathione transferase domain - Study of a diverse, ancient protein superfamily using motif search and structural modeling. Protein Sci. 3: 2045-2054.
14. Kyrpides, N. C., Olsen, G. J., Klenk, H.-P., White, O., and Woese, C. R. (1996). Methanococcus jannaschii genome: Revisited. Microb. Comp. Genomics 1: 329-338.
15. Pearson, W. R. (1990). Rapid and sensitive sequence comparison with FASTP and FASTA. In "Methods in Enzymology" (R. F. Doolittle, Ed.), Vol. 183, pp. 63-98, Academic Press San Diego.
16. Pearson, W. R. (1995). Comparison of methods for searching protein sequence databases. Protein Sci. 4: 1145-1160.
17. Pearson, W. R. (1996). Effective protein sequence comparison. Methods Enzymol. 266: 227-258.
18. Pearson, W. R., and Lipman, D. J. (1988). Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85: 2444-2448.
19. Peltola, H., Soderlund, H., and Ukkonen, E. (1986). Algorithms for the search of amino acid patterns in nucleic acid sequences. Nucleic Acids Res. 14: 99-107.
20. Robison, K., Gilbert, W., and Church, G. M. (1996). More Haemophilus and Mycoplasma genes. Science 271: 1302-1303.
21. Wootton, J. C. (1994). Non-globular domains in protein sequences: Automated segmentation using complexity measures. Comput. Chem. 18: 269-285.
22. Zhang, Z., Pearson, W., and Miller, W. (1997). Aligning a DNA sequence with a protein sequence. J. Comput. Biol. 4: 337-343.