ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs

Improved-Bidirectional Exact Pattern Matching

In this research, we present an improved version of Bidirectional (BD) exact pattern matching (EPM) algorithm to solve the problem of exact pattern matching. Improved-Bidirectional (IBD) exact pattern matching algorithm introduced a new idea of scanning partial text window (PTW) as well with the pattern to take decision of moving pattern to the right of partial text window. IBD algorithm compar...

Improved Approach for Exact Pattern Matching

In this research we present Bidirectional exact pattern matching algorithm [20] in detail. Bidirectional (BD) exact pattern matching (EPM) introduced a new idea to compare pattern with Selected Text Window (STW) of text string by using two pointers (right and left) simultaneously in searching phase. In preprocessing phase Bidirectional EPM algorithm improved the shift decision by comparing righ...

Discovering Themes by Exact Pattern Matching

1. INTRODUCTION Content-based music information retrieval provides ways for people to locate and retrieve music based on its musical characteristics, rather than on more familiar metadata such as composer and title. The potential utility of such systems is attested to by music librarians, who report that library patrons often hum or whistle a phrase of music and ask them to identify the corresp...

Exact Pattern Matching for RNA Structure Ensembles

ExpaRNA’s core algorithm computes, for two fixed RNA structures, a maximal non-overlapping set of maximal exact matchings. We introduce an algorithm ExpaRNA-P that solves the lifted problem of finding such sets of exact matchings in entire Boltzmann-distributed structure ensembles of two RNAs. Due to a novel kind of structural sparsification, the new algorithm maintains the time and space compl...

Exact Pattern Matching for RNA Secondary Structures