Bidirectional string anchors: A new string sampling mechanism

Abstract

The minimizers sampling mechanism is a popular mechanism for string sampling introduced independently by Schleimer et al. [SIGMOD 2003] and by Roberts et al. [Bioinf. 2004]. Given two positive integers w and k, it selects the lexicographically smallest length-k substring in every fragment of w consecutive length-k substrings (in every sliding window of length w+k-1). Minimizers samples are approximately uniform, locally consistent, and computable in linear time. Although they do not have good worst-case guarantees on their size, they are often small in practice. They thus have been successfully employed in several string processing applications. Two main disadvantages of minimizers sampling mechanisms are: first, they also do not have good guarantees on the expected size of their samples for every combination of w and k; and, second, indexes that are constructed over their samples do not have good worst-case guarantees for on-line pattern searches. To alleviate these disadvantages, we introduce bidirectional string anchors (bd-anchors), a new string sampling mechanism. Given a positive integer , our mechanism selects the lexicographically smallest rotation in every length- fragment (in every sliding window of length ). We show that bd-anchors samples are also approximately uniform, locally consistent, and computable in linear time. In addition, our experimen