Abstract
The oldest and still the single most frequent “bioinformatic” activity is the comparison of nucleotide or protein sequences, nowadays usually as part of a search for matches in large databanks. Despite the fact that it also involves differences between two linear orderings, the comparison of gene orders is a completely different enterprise. Sequence comparison pertains to strings of symbols drawn from a small alphabet, so that each symbol appears many times, whereas gene order comparisons compare permutations of n symbols, each symbol appearing only once (in the simplest case). Sequence comparison assumes that the strings being compared diverged through local changes such as substitution, insertion, and deletion, whereas gene orders diverged through rearrangement operations, such as inversion, transposition and translocation, affecting any number of terms.
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Sankoff, D., Nadeau, J.H. (2000). A New Set of Problems for a New Kind of Data. In: Sankoff, D., Nadeau, J.H. (eds) Comparative Genomics. Computational Biology, vol 1. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-4309-7_15
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DOI: https://doi.org/10.1007/978-94-011-4309-7_15
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