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String Mathematics, BLAST, and FASTA

  • Xuhua Xia
Chapter

Abstract

What is an e-value for ungapped and gapped BLAST? What are the Karlin-Altschul parameters that affect e-value calculation? How nucleotide frequencies and match-mismatch matrices affect such parameters? What are the key algorithms for FASTA and BLAST? How do their differences affect sensitivity of sequence search? This chapter addresses these questions and illustrates applications of string matching in genomics, transcriptomics, and proteomics, as well as in drug discovery.

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© Springer Science+Business Media LLC 2018

Authors and Affiliations

  • Xuhua Xia
    • 1
  1. 1.University of Ottawa CAREG and Biology DepartmentOttawaCanada

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