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Algorithms on Strings, Trees and Sequences by Dan Gusfield

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14

Multiple String Comparison – The Holy Grail

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In this chapter we begin the discussion of multiple string comparison, one of the most important methodological issues and most active research areas in current biological sequence analysis. We first discuss some of the reasons for the importance of multiple string comparison in molecular biology. Then we will examine multiple string alignment, one common way that multiple string comparison has been formalized. We will precisely define three variants of the multiple alignment problem and consider in depth algorithms for attacking those problems. Other variants will be sketched in this chapter; additional ...

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