@inproceedings{11c252b8cf364796bb2386bfd45f2cb6,

title = "K-mismatch with don't cares",

abstract = "We give the first non-trivial algorithms for the k-mismatch pattern matching problem with don't cares. Given a text t of length n and a pattern p of length m with don't care symbols and a bound k, our algorithms find all the places that the pattern matches the text with at most k mismatches. We first give an O(n(k + log n log log n) log m) time randomised solution which finds the correct answer with high probability. We then present a new deterministic O(nk2 log3 m) time solution that uses tools developed for group testing and finally an approach based on k-selectors that runs in O(nk polylog m) time but requires O(poly m) time preprocessing. In each case, the location of the mismatches at each alignment is also given at no extra cost.",

author = "Rapha{\"e}l Clifford and Klim Efremenko and Ely Porat and Amir Rothschild",

year = "2007",

month = jan,

day = "1",

doi = "10.1007/978-3-540-75520-3_15",

language = "English",

isbn = "9783540755197",

series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

publisher = "Springer Verlag",

pages = "151--162",

booktitle = "Algorithms - ESA 2007 - 15th Annual European Symposium, Proceedings",

address = "Germany",

note = "15th Annual European Symposium on Algorithms, ESA 2007 ; Conference date: 08-10-2007 Through 10-10-2007",

}