Sequence analysis using GCG

Methods of Biochemical Analysis

Volumn 39, Issue , 1998, Pages 74-97

  Butler, Barbara A ^a  

^a Genetics Computer Group Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BIOLOGY; COMPUTER PROGRAM; CONSENSUS SEQUENCE; FACTUAL DATABASE; GENETICS; METHODOLOGY; MOLECULAR GENETICS; OPEN READING FRAME; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; CONSENSUS SEQUENCE; DATABASES, FACTUAL; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PHYLOGENY; PROTEINS; RNA, MESSENGER; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SOFTWARE;

EID: 0031634714     PISSN: 00766941     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Article

References (26)

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. Bairoch, A., and Apweiler, R. (1997). The SWISS-PROT protein data bank and its supplement TrEMBL. Nucl. Acids Res. 25, 31-36.
3. Bairoch, A., Bucher, P., and Hofmann, K. (1997). The PROSITE Database: Its status in 1997. Nucl. Acids Res. 25, 217-221.
4. Benson, D. A., Boguski, M. S., Lipman, D. J., and Ostell, J. (1997). GenBank. Nucl. Acids Res. 25, 1-6.
5. Chou, P. Y., and Fasman, G. D. (1978). Prediction of the secondary structure of proteins from their amino acid sequence. Adv. Enzymol. 47, 45-147.
6. Etzold, T., and Argos, P. (1993). SRS - An indexing and retrieval tool for flat file data libraries. Comput. Appl. Bioscie. 9, 49-57.
7. Etzold, T., Ulyanov, A., and Argos, P. (1996). SRS: Information retrieval system for molecular biology data banks. Methods Enzymol. 266, 114-128.
8. Fickett, J. (1982). Recognition of protein coding regions in DNA sequences. Nucl. Acids Res. 10, 5303-5318.
9. George, D. G., Dodson, R. J., Garavelli, J. S., Haft, D. H., Hunt, L. T., Marzec, C. R., Orcutt, B. C., Sidman, K. E., Srinivasarao, G. Y., Yeh, L. L., Arminski, L. M., Ledley, R. S., Tsugita, A., and Barker, W. C. (1997). The Protein Information Resource (PIR) and the PIR-International Protein Sequence Database. Nucl. Acids Res. 25, 24-27.
10. Gilbert, W. (1981). DNA sequencing and gene structure. Science 214, 1305-1312.
11. Gribskov, M., Devereux, J. D., and Burgess, R. R. (1983). The codon preference plot: Graphic analysis of protein coding sequences and prediction of gene expression. Nucl. Acids Res. 12, 539-549.
12. Gribskov, M., McLachlan, M., and Eisenberg, D. (1987). Profile analysis: Detection of distantly related proteins. Proc. Natl. Acad. Sci. U.S.A. 84, 4355-4358.
13. Gribskov, M., Luthy, R., and Eisenberg, D. (1990). Profile analysis. Methods Enzymol. 183, 146-159.
14. Higgins, D., Thompson, J. D., and Gibson, T. C. (1996). Using CLUSTAL for Multiple Sequence Alignments. Methods Enzymol. 183, 383-402.
15. Li, W. H. (1993). Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36, 96-99.
16. Needleman, S. B., and Wunsch, C. D. (1970). A general method applicable to the search for similarities in the amino acid sequences of two proteins. J. Mol. Biol. 48, 443-453.
17. Pamilo, P., and Bianchi, N. O. (1993). Evolution of the Zfx and Zfy genes: Rates and interdependence between the genes. Mol. Biol. Evol. 10, 271-281.
18. Pearson, W. R. (1990). Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol. 183, 63-98.
19. Pearson, W. R. (1996). Effective protein sequence comparison. Methods Enzymol. 266, 227-258.
20. Pearson, W. R., and Lipman, D. J. (1988). Improved tools for biological sequence analysis. Proc. Natl. Acad. Sci. U.S.A. 85, 2444-2448.
21. Sanger, F. (1981). Determination of nucleotide sequences in DNA. Science 214, 1205-1210.
22. Smith, T. F., and Waterman, M. S. (1981). Comparison of bio-sequences. Adv. Appl. Math. 2, 482-489.
23. Staden, R. (1980). A new computer method for the storage and manipulation of DNA gel reading data. Nucl. Acids Res. 8, 3673-3694.
24. Stoesser, G., Sterk, P., Tuli, M. A., Stoehr, P. J., and Cameron, G. N. (1997). The EMBL Nucleotide Sequence Database. Nucl. Acids Res. 25, 7-13.
25. Swofford, D. (1996). PAUP*: Phylogenetic Analysis Using Parsimony (and Other Methods), version 4.0 (Sunderland, MA: Sinauer Associates).
26. Zuker, M. (1989). On finding all suboptimal foldings on an RNA molecule. Science 244, 48-52.