Computer Analysis of Sequence Data

Volume 25 of the series Methods in Molecular Biology pp 365-389

Using the FASTA Program to Search Protein and DNA Sequence Databases

  • William R. PearsonAffiliated withDepartment of Biochemistry, University of Virginia

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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).