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During the past several years, the use of computer programs in the analysis of protein and DNA sequences has become commonplace. In all but the simplest procedures, the ability to critically review the results obtained with computer methods requires a basic knowledge of the algorithms employed (and the assumptions upon which they are based), an awareness of the capabilities and limitations of the particular program that implements an algorithm, and some familiarity with probability and statistics. We describe a number of computer methods that have been applied to the analysis of apolipoprotein sequences. We discuss the suitability of these methods for particular problems, how the choice of initial "parameters" can affect the results, and what the results can tell us about protein or gene sequences. We also identify some outstanding problems of apolipoprotein sequence analysis where further work is needed.
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