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Updated: Jul 9, 2026

Determining the Role of Maternally-Expressed Genes in Early Development with Maternal Crispants
Published on: December 21, 2021
Incorporating indel channels into average-case analysis of seed-chain-extend
Spencer Gibson1, Yun William Yu2
1Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, United States.
Motivation:
Given a sequence s1 of n letters drawn independently and identically (i.i.d.) from an alphabet of size σ and a mutated substring s2 of length m
Results:
We introduce mathematical machinery to deal with the two new obstacles introduced by indel channels: the dependence of neighbouring anchors and the presence of anchors that are only partially correct. We prove that expected recoverability of an optimal chain is ≥1-O(1m) and expected runtime is O(mn3.15·θT log n), given the total mutation rate θT=θi+θd+θs (sum of substitution, insertion, and deletion rates) is θT≤0.159. We thus narrow (but not close) the gap between theory and practice.
Availability And Implementation:
https://github.com/Lazarus42/seed_chainer_indels.
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