A repetitive sequence collection is one where portions of a base sequence of length n are repeated many times with small variations, forming a collection of total length N . Examples of such collections are version control data and genome sequences of individuals, where the differences can be expressed by lists of basic edit operations. Flexible and efficient data analysis on a such typically h...

In this paper, we consider a setting where aclient wants to outsource storage of a large amount ofprivate data and then perform substring search querieson the data – given a data string s and a search stringp, find all occurrences of p as a substring of s. First, weformalize an encryption paradigm that we call queryableencryption, which generalizes searchable symmetric e...

In this paper, we consider a setting where a client wants to outsource storage of a large amount of private data and then perform substring search queries on the data – given a data string s and a search string p, find all occurrences of p as a substring of s. First, we formalize an encryption paradigm that we call queryable encryption, which generalizes searchable symmetric encryption (SSE) an...

In this section we will introduce suffix trees, which, among many other things, can be used to solve the string matching task (find pattern P of length m in a text T of length n in O(n+m) time). In the exercises, we have already seen that other methods (Boyer-Moore, e.g.) solve this task in the same time. So why do we need suffix trees? The advantage of suffix trees over the other string-matchi...

In this paper, we consider a setting where a client wants to outsource storage of a large amount of private data and then perform substring search queries on the data – given a data string s and a search string p, find all occurrences of p as a substring of s. First, we formalize an encryption paradigm that we call queryable encryption, which generalizes searchable symmetric encryption (SSE) an...

A suffix tree is a fundamental data structure for string searching algorithms. Unfortunately, when it comes to the use of suffix trees in real-life applications, the current methods for constructing suffix trees do not scale for large inputs. As suffix trees are larger than the input sequences and quickly outgrow the main memory, the first attempts at building large suffix trees focused on algo...