Alignment
9
Melanie Kappelmann-Fenzl
Contents
9.1 Introduction . . . . . .. . . .. . . .. . . .. . .. . . .. . . .. . . .. . .. . . .. . . .. . . .. . . .. . .. . . .. . . .. . . .. . .. . . .. . . .. . . .. 112
9.2 Alignment Definition . . . .. . . .. . . .. . . .. . . .. . . .. . . .. . . .. . . .. . . .. . . .. . . .. . . .. . . .. . . .. . . .. . . .. . . .. 112
9.2.1 Global Alignment (Needleman–Wunsch Algorithm) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
9.2.2 Local Alignment (Smith–Waterman Algorithm) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
9.2.3 Alignment Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
What You Will Learn in This Chapter
The purposes of the alignment process are to measure distances/similarities between
strings and thus to locate origins of Next Generation Sequencing (NGS) reads in a
reference genome. Alignment algorithms like BLAST that can be used to search for
the location of a single or a small number of sequences in a certain genome are not
(continued)
M. Kappelmann-Fenzl (*)
Deggendorf Institute of Technology, Deggendorf, Germany
Institute of Biochemistry (Emil-Fischer Center), Friedrich-Alexander University Erlangen-Nürnberg,
Erlangen, Germany
e-mail: melanie.kappelmann-fenzl@th-deg.de
# Springer Nature Switzerland AG 2021
M. Kappelmann-Fenzl (ed.), Next Generation Sequencing and Data Analysis, Learning
Materials in Biosciences, https://doi.org/10.1007/978-3-030-62490-3_9
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