Computing Maximal Covers for Protein Sequences

A partial cover of a string or sequence of length n, which we model as an array $x=x\left[1..n\right]$, is a repeating substring u of x such that "many" positions in x lie within occurrences of u. A maximal cover u*-introduced in 2018 by Mhaskar and Smyth as optimal cover-is a partial cover that, over all partial covers u, maximizes the positions covered. Applying data structures also introduced by Mhaskar and Smyth, our software MAXCOVER for the first time …