Abstract
We’ve seen that optimal alignment is slow but accurate while exact matching is fast but cannot account for mutations. In this Chapter we tweak exact matching to get fast alignments. We begin with the easiest case, global alignment between a query and a subject of similar lengths. Then we move to the best known application of fast alignment, local alignment between a short query and a long subject as implemented in Blast.
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© 2023 The Author(s), under exclusive license to Springer Nature Switzerland AG
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Haubold, B., Börsch-Haubold, A. (2023). Fast Alignment. In: Bioinformatics for Evolutionary Biologists. Springer, Cham. https://doi.org/10.1007/978-3-031-20414-2_4
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DOI: https://doi.org/10.1007/978-3-031-20414-2_4
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Publisher Name: Springer, Cham
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