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A method for classifying unaligned biological sequences

  • B. Tallur
  • J. Nicolas
Conference paper
Part of the Studies in Classification, Data Analysis, and Knowledge Organization book series (STUDIES CLASS)

Summary

It is needless to emphasize the importance of classification of protein sequences in molecular biology. Various methods of classification are currently being used by biologists (Landès et aí.1992) but most of them require the sequences to be prealigned — and thus to be of equal length — using one of the several multiple alignment algorithms available, so as to make the site-by-site comparison of sequences possible. Two LLA-based approaches for classifying prealigned sequences were already proposed (Lerman et al. (1994a)) whose results compared favourably with most currently used methods. The first approach made use of the “preordonnance” coding and the second one, the idea of “significant windows”. The new directions of research leading to a clustering method free from this somewhat strong constraint were also suggested by the authors. The present paper gives an account of the recent developments of our research, consisting of a new method that gets round the sequence comparison problem faced with while dealing with unaligned sequences, thanks to the “significant windows” approach.

Keywords

Window Size Sequence Pair Beam Search Letter Pair Significant Window 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer Japan 1998

Authors and Affiliations

  • B. Tallur
    • 1
  • J. Nicolas
    • 1
  1. 1.Campus Universitaire de BeaulieuIRISARennes cedexFrance

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