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© IRL Press Limited

Compression of nucleic acid and protein sequence data

J. Richard Walker and Peter Willett *

Department of Information Studies, University of Sheffield Western Bank, Sheffield S10 2TN, UK

*To whom reprint requests should be sent.

This paper describes the application of text compression methods to machine-readable files of nucleic acid and protein sequence data. Two main methods are used to reduce the storage requirements of such files, these being n-gram coding and run-length coding. A Pascal program combining both of these techniques resulted in a compression figure of 74.6% for the GenBank database and a program that used only n-gram coding gave a compression figure of 42.8% for the Protein Identification Resource database.

Received on November 29, 1985; accepted on February 24, 1986

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