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Computing string or sequence alignments is a classical method of comparingstrings and has applications in many areas of computing, such as signalprocessing and bioinformatics. Semi-local string alignment is a recentgeneralisation of this method, in which the alignment of a given string and allsubstrings of another string are computed simultaneously at no additionalasymptotic cost. In this paper, we show that there is a close connectionbetween semi-local string alignment and a certain class of traditionalcomparison networks known as transposition networks. The transposition networkapproach can be used to represent different string comparison algorithms in aunified form, and in some cases provides generalisations or improvements onexisting algorithms. This approach allows us to obtain new algorithms forsparse semi-local string comparison and for comparison of highly similar andhighly dissimilar strings, as well as of run-length compressed strings. Weconclude that the transposition network method is a very general and flexibleway of understanding and improving different string comparison algorithms, aswell as their efficient implementation.

String comparison by transposition networks