Practical colinear chaining on sequences revisited

Abstract

Colinear chaining is a classical heuristic for sequence alignment and is widely used in modern practical aligners. Jain et al. (J. Comput. Biol. 2022) proposed an $O(n \log^3 n)$ time algorithm to chain a set of $n$ anchors so that the chaining cost matches the edit distance of the input sequences, when anchors are all the maximal exact matches. Moreover, assuming a uniform and sparse distribution of anchors, they provided a practical solution ($\mathtt{ChainX}$) working in $O(n \cdot \mathrm{SOL} + n \log n)$ average-case time, where $\mathrm{SOL}$ is the cost of the output chain. This practical solution is not guaranteed to be optimal: we study the failing cases, introduce the anchor diagonal distance, and find and implement an optimal algorithm working in $O(n \cdot \mathrm{OPT} + n \log n)$ average-case time, where $\mathrm{OPT}$ $\le \mathrm{SOL}$ is the optimal chaining cost. We validate the results by Jain et al., show that $\mathtt{ChainX}$ can be suboptimal with a realistic long read dataset, and show minimal computational slowdown for our solution.