Search results for "Wildcard character"
showing 4 items of 4 documents
Indexing a sequence for mapping reads with a single mismatch
2014
Mapping reads against a genome sequence is an interesting and useful problem in computational molecular biology and bioinformatics. In this paper, we focus on the problem of indexing a sequence for mapping reads with a single mismatch. We first focus on a simpler problem where the length of the pattern is given beforehand during the data structure construction. This version of the problem is interesting in its own right in the context of the next generation sequencing. In the sequel, we show how to solve the more general problem. In both cases, our algorithm can construct an efficient data structure in time and space and can answer subsequent queries in time. Here, n is the length of the s…
Multi-Dimensional Pattern Matching with Dimensional Wildcards: Data Structures and Optimal On-Line Search Algorithms
1997
We introduce a new multidimensional pattern matching problem that is a natural generalization of string matching, a well studied problem1. The motivation for its algorithmic study is mainly theoretical. LetA1:n1,?,1:nd be a text matrix withN=n1?ndentries andB1:m1,?,1:mr be a pattern matrix withM=m1?mrentries, whered?r?1 (the matrix entries are taken from an ordered alphabet ?). We study the problem of checking whether somer-dimensional submatrix ofAis equal toB(i.e., adecisionquery).Acan be preprocessed andBis given on-line. We define a new data structure for preprocessingAand propose CRCW-PRAM algorithms that build it inO(logN) time withN2/nmaxprocessors, wherenmax=max(n1,?,nd), such that …
Quantum algorithms for search with wildcards and combinatorial group testing
2012
We consider two combinatorial problems. The first we call "search with wildcards": given an unknown n-bit string x, and the ability to check whether any subset of the bits of x is equal to a provided query string, the goal is to output x. We give a nearly optimal O(sqrt(n) log n) quantum query algorithm for search with wildcards, beating the classical lower bound of Omega(n) queries. Rather than using amplitude amplification or a quantum walk, our algorithm is ultimately based on the solution to a state discrimination problem. The second problem we consider is combinatorial group testing, which is the task of identifying a subset of at most k special items out of a set of n items, given the…
Multi-dimensional pattern matching with dimensional wildcards
1995
We introduce a new multi-dimensional pattern matching problem, which is a natural generalization of the on-line search in string matching. We are given a text matrix A[1: n1, ..., 1:n d ] of size N= n1×n2×...×n d , which we may preprocess. Then, we are given, online, an r-dimensional pattern matrix B[1:m1,...,1:m r ] of size M= m1×m2×...×m r , with 1≤r≤d. We would like to know whether B*=B*[*, 1:m1,*, ...,1: mr, *] occurs in A, where * is a dimensional wildcard such that B* is any d-dimensional matrix having size 1 × ... × m1×...1×m r ×...1 and containing the same elements as B. Notice that there might be (d/r)≤2d occurrences of B* for each position of A. We give CRCW-PRAM algorithms for pr…