Related papers: Motif matching using gapped patterns
We describe indexes for searching large data sets for variable-length-gapped (VLG) patterns. VLG patterns are composed of two or more subpatterns, between each adjacent pair of which is a gap-constraint specifying upper and lower bounds on…
We study distributed algorithms for string matching problem in presence of wildcard characters. Given a string T (a text), we look for all occurrences of another string P (a pattern) as a substring of string T . Each wildcard character in…
We present a new algorithm for subsequence matching in grammar compressed strings. Given a grammar of size $n$ compressing a string of size $N$ and a pattern string of size $m$ over an alphabet of size $\sigma$, our algorithm uses…
In this paper, we consider the problem of identifying patterns of interest in colored strings. A colored string is a string where each position is assigned one of a finite set of colors. Our task is to find substrings of the colored string…
A string matching -- and more generally, sequence matching -- algorithm is presented that has a linear worst-case computing time bound, a low worst-case bound on the number of comparisons (2n), and sublinear average-case behavior that is…
String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…
Approximate pattern matching is a natural and well-studied problem on strings: Given a text $T$, a pattern $P$, and a threshold $k$, find (the starting positions of) all substrings of $T$ that are at distance at most $k$ from $P$. We…
Sequence discovery tools play a central role in several fields of computational biology. In the framework of Transcription Factor binding studies, motif finding algorithms of increasingly high performance are required to process the big…
The search for patterns or motifs in data represents a problem area of key interest to finance and economic researchers. In this paper we introduce the Motif Tracking Algorithm, a novel immune inspired pattern identification tool that is…
In runtime verification, pattern matching, which searches for occurrences of a specific pattern within a word, provides more information than a simple violation detection of the monitored property, by locating concrete evidence of the…
We introduce a new string matching problem called order-preserving matching on numeric strings where a pattern matches a text if the text contains a substring whose relative orders coincide with those of the pattern. Order-preserving…
The classical pattern matching asks for locating all occurrences of one string, called the pattern, in another, called the text, where a string is simply a sequence of characters. Due to the potential practical applications, it is desirable…
The problem of finding factors of a text string which are identical or similar to a given pattern string is a central problem in computer science. A generalised version of this problem consists in implementing an index over the text to…
The abelian pattern matching problem consists in finding all substrings of a text which are permutations of a given pattern. This problem finds application in many areas and can be solved in linear time by a naive sliding window approach.…
A pattern $\alpha$ is a string of variables and terminal letters. We say that $\alpha$ matches a word $w$, consisting only of terminal letters, if $w$ can be obtained by replacing the variables of $\alpha$ by terminal words. The matching…
The classic string indexing problem is to preprocess a string S into a compact data structure that supports efficient pattern matching queries. Typical queries include existential queries (decide if the pattern occurs in S), reporting…
Exact string matching has been a fundamental problem in computer science for decades because of many practical applications. Some are related to common procedures, such as searching in files and text editors, or, more recently, to more…
In this work, we tackle a natural variation of the String Matching Problem on the case of a dynamic pattern, that is, given a static text $T$ and a pattern $P$, we want to support character additions and deletions to the pattern, and after…
We revisit the complexity of approximate pattern matching in an elastic-degenerate string. Such a string is a sequence of $n$ finite sets of strings of total length $N$, and compactly describes a collection of strings obtained by first…
The NP-complete Permutation Pattern Matching problem asks whether a permutation P (the pattern) can be matched into a permutation T (the text). A matching is an order-preserving embedding of P into T. In the Generalized Permutation Pattern…