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Quality of Algorithms for Sequence Comparison

  • Mikhail Roytberg
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6744)

Abstract

Pair-wise sequence alignment is the basic method of comparative analysis of proteins and nucleic acids. Studying the results of the alignment one has to consider two questions: (1) did the program find all the interesting similarities (“sensitivity”) and (2) are all the found similarities interesting (“selectivity”). Definitely, one has to specify, what alignments are considered as the interesting ones. Analogous questions can be addressed to each of the obtained alignments: (3) which part of the aligned positions are aligned correctly (“confidence”) and (4) does alignment contain all pairs of the corresponding positions of compared sequences (“accuracy”). Naturally, the answer on the questions depends on the definition of the correct alignment. The presentation addresses the above two pairs of questions that are extremely important in interpreting of the results of sequence comparison.

Keywords

alignment seed sequence comparison sensitivity selectivity accuracy confidence 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Mikhail Roytberg
    • 1
    • 2
  1. 1.Institute of Mathematical Problems in BiologyRASMoscow RegionRussia
  2. 2.National Research University Higher School of EconomicsMoscowRussia

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