Approximate string matching with reduced alphabet

Peer reviewe

Parallel Quick-Skip Search Hybrid Algorithm For The Exact String Matching Problem.

Masalah padanan rententan merupakan mercu tanda dalam kebanyakan bidang sains komputer kerana peranan yang dimainkannya dalam pelbagai aplikasi komputer. The string matching problem occupies a corner stone in many computer science fields because of the fundamental role it plays in various computer applications

Parallel String Matching with Multi Core Processors-A Comparative Study for Gene Sequences

The increase in huge amount of data is seen clearly in present days because of requirement for storing more information. To extract certain data from this large database is a very difficult task, including text processing, information retrieval, text mining, pattern recognition and DNA sequencing. So we need concurrent events and high performance computing models for extracting the data. This will create a challenge to the researchers. One of the solutions is parallel algorithms for string matching on computing models. In this we implemented parallel string matching with JAVA Multi threading with multi core processing, and performed a comparative study on Knuth Morris Pratt, Boyer Moore and Brute force string matching algorithms. For testing our system we take a gene sequence which consists of lacks of records. From the test results it is shown that the multicore processing is better compared to lower versions. Finally this proposed parallel string matching with multicore processing is better compared to other sequential approaches

Boyer-Moore strategy to efficient approximate string matching

International audienceWe propose a simple but e cient algorithm for searching all occurrences of a pattern or a class of patterns (length m) in a text (length n) with at most k mismatches. This algorithm relies on the Shift-Add algorithm of Baeza-Yates and Gonnet [6], which involves representing by a bit number the current state of the search and uses the ability of programming languages to handle bit words. State representation should not, therefore, exceeds the word size w, that is, m(⌈log2(k+1)⌉+1 )≤w. This algorithm consists in a preprocessing step and a searching step. It is linear and performs 3n operations during the searching step. Notions of shift and character skip found in the Boyer-Moore (BM) [9] approach, are introduced in this algorithm. Provided that the considered alphabet is large enough (compared to the Pattern length), the average number of operations performed by our algorithm during the searching step becomes n(2+(k+4)/(m-k))

Mutable strings in Java: design, implementation and lightweight text-search algorithms

AbstractThe Java string classes, String and StringBuffer, lie at the extremes of a spectrum (immutable, reference based, and mutable, content based). Analogously, available text-search methods on string classes are implemented either as trivial, brute-force double loops, or as very sophisticated and resource-consuming regular-expression search methods. Motivated by our experience in data-intensive text applications, we propose a new string class, MutableString, which tries to get the right balance between extremes in both cases. Mutable strings can be in one of two states, compact and loose, in which they behave more like String and StringBuffer, respectively. Moreover, they support a wide range of sophisticated text-search algorithms with a very low resource usage and set-up time, using a new, very simple randomised data structure (a generalisation of Bloom filters) that stores an approximation from above of a lattice-valued function. Computing the function value requires a constant number of steps, and the error probability can be balanced with space usage. As a result, we obtain practical implementations of Boyer–Moore type algorithms that can be used with very large alphabets, such as Unicode collation elements. The techniques we develop are very general and amenable to a wide range of applications