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Computer Analysis of Amino Acid Sequences

The Case of Plant Virus Capsid Proteins

  • Protocol
Plant Virology Protocols

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 81))

Abstract

Genome sequences are of minimal use without an adequate interpretation of the sequences of putative protein products, which is only possible on the basis of detailed computer analysis. The approaches to amino acid sequence analysis can be roughly divided into those that explore intrinsic properties of proteins, such as hydropathy, secondary structure, distribution of different types of amino acid sequences, and so on, and those that search for sequence similarity. Both approaches include numerous algorithms and computer programs. In this short chapter, we cannot describe all or even the most widely used and valuable of these methods. Instead, we present a minimal set of procedures that, in our experience, is useful in order to extract a substantial amount of information from an amino acid sequence in a relatively short time. For detailed descriptions of various computer methods for sequence analysis, the reader is referred to the recently published reviews and Methods in Enzymology collections (1–3).

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Notes

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Author information

Authors and Affiliations

  1. Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD

    Eugene V. Koonin & Arcady R. Mushegian

  2. Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR

    Valerian V. Dolja

Authors
  1. Eugene V. Koonin
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  2. Arcady R. Mushegian
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  3. Valerian V. Dolja
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Editor information

Editors and Affiliations

  1. Plant Virology Group School of Biological Sciences, University of Bristol, UK

    Gary D. Foster

  2. Department of Botany, University of Leicester, UK

    Gary D. Foster  & Sally C. Taylor  & 

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© 1998 Humana Press Inc.

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Koonin, E.V., Mushegian, A.R., Dolja, V.V. (1998). Computer Analysis of Amino Acid Sequences. In: Foster, G.D., Taylor, S.C. (eds) Plant Virology Protocols. Methods in Molecular Biology™, vol 81. Humana Press. https://doi.org/10.1385/0-89603-385-6:319

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  • DOI: https://doi.org/10.1385/0-89603-385-6:319

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-385-6

  • Online ISBN: 978-1-59259-566-2

  • eBook Packages: Springer Protocols

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