Making Sense of Score Statistics for Sequence Alignments

  title={Making Sense of Score Statistics for Sequence Alignments},
  author={Marco Pagni and C. Victor Jongeneel},
  journal={Briefings in bioinformatics},
  volume={2 1},
The search for similarity between two biological sequences lies at the core of many applications in bioinformatics. This paper aims to highlight a few of the principles that should be kept in mind when evaluating the statistical significance of alignments between sequences. The extreme value distribution is first introduced, which in most cases describes the distribution of alignment scores between a query and a database. The effects of the similarity matrix and gap penalty values on the score… CONTINUE READING
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