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Sequence similarity (‘Homology’) searching for molecular biologists

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Abstract

Major types of sequence similarity searching (often, and incorrectly, called ‘homology’ searching) are reviewed and examples of each are presented. The features and limitations of each type of program, and individual implementations of each type are discussed. Two pairs of sequences are used as examples to show how implementations of each type differ in their results and their presentation. Both local and global alignment programs are examined, and the programs reviewed run on many different types of computer architectures, from laboratory computers such as the IBM PC, minicomputers such as the VAX, to large mainframe computers such as DEC-10/20 series.

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  1. Dan Davison

    Present address: Department of Biochemical and Biophysical Sciences, Science and Research No. 1, University of Houston, University Park, 77004, Houston, TX, U.S.A.

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  1. Graduate Program in Genetics, State University of New York at Stony Brook, 11794, Stony Brook, NY, U.S.A.

    Dan Davison

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Davison, D. Sequence similarity (‘Homology’) searching for molecular biologists. Bltn Mathcal Biology 47, 437–474 (1985). https://doi.org/10.1007/BF02460006

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