Abstract
As this volume illustrates, computers have become an integral tool in the analysis of DNA and protein sequence data. One of the most popular applications of computers in modern molecular biology is to characterize newly determined sequences by searching DNA and protein sequence databases. The FASTA* program (1,2) is widely used for such searches, because it is fast, sensitive, and readily available. FASTA is available as part of a package of programs that construct local and global sequence alignments. This chapter will describe a number of simple applications of FASTA and other programs in the FASTA package. This chapter focuses on the steps required to run the programs, rather than on the interpretation of the results of a FASTA search. For a more complete description of FASTA and related programs for identifying distantly related DNA and protein sequences, for evaluating the statistical significance of sequence similarities, and for identifying similar structures in DNA and protein sequences see ref. 2.
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Pearson, W. R. and Lipman, D. I. (1988) Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85, 2444–2448.
Pearson, W. R. (1990) Rapid and sensitive sequence comparison with FASTP and FASTA, in Methods in Enzymology, vol. 183 (Doolittle, R. F, ed.), Academic, New York, pp. 63–98.
Lipman, D. J. and Pearson, W. R. (1985) Rapid and sensitive protem similarity searches. Science 227, 1435–1441.
Pearson, W. R. (1991) Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics 11, 635–650.
Dayhoff, M., Schwartz, R. M., and Orcutt, B. C. (1978) A model of evolutionary change in proteins, in Atlas of Protein Sequence and Structure, vol. 5,supplement 3 (Dayhoff, M, ed.), National Biomedical Research Foundation, Silver Spring, MD, pp. 345–352.
Doolittle, R. F., Feng, D. F., Johnson, M. S., and McClure, M. A. (1986) Relationships of human protein sequences to those of other organisms. Cold Spring Harb. Symp. Quant. Biol. 51, 447–455.
Smith, T. F. and Waterman, M. S. (1981) Identification of common molecular subsequences. J. Mol. Biol. 147, 195–197.
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990) A basic local alignment search tool. J. Mol. Biol. 215, 403–410.
Waterman, M. S. and Eggert, M. (1987) A new algorithm for best subsequences alignment with application to tRNA-rRNA comparisons. J. Mol. Biol. 197, 723–728.
Huang, X., Hardrson, R. C., and Miller, W. (1990) A space-efficient algorithm for local similarities. CABIOS 6, 373–381.
Huang, X. and Miller, W. (1991) A time-efficient, linear-space local similarity algorithm. Adv. Appl. Math. 12, 337–357.
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© 1994 Humana Press Inc., Totowa, NJ
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Pearson, W.R. (1994). Using the FASTA Program to Search Protein and DNA Sequence Databases. In: Griffin, A.M., Griffin, H.G. (eds) Computer Analysis of Sequence Data. Methods in Molecular Biology, vol 24. Humana Press. https://doi.org/10.1385/0-89603-246-9:307
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DOI: https://doi.org/10.1385/0-89603-246-9:307
Publisher Name: Humana Press
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