BNDM Algorithm Research Articles

Searching long patterns with BNDM

AbstractWe present new algorithms for exact string matching of long patterns. Our algorithms read ‐grams at constant distances and are variations of the simplified BNDM algorithm. We demonstrate the competitiveness of our solutions through practical experiments. Many of our algorithms were faster than previous methods for English and DNA patterns between 400 and 50,000 in length. Our algorithms were still better when the preprocessing time was taken into account or when the patterns were taken from a different text of the same type.

String matching with lookahead

Forward-SBNDM is a recently introduced variation of the BNDM algorithm for exact string matching. Forward-SBNDM inspects a 2-gram in the text such that the first character is the last one of an alignment window of the pattern and the second one is then outside the window. We present a generalization of this idea by inspecting several lookahead characters beyond an alignment window and integrate it with SBNDMq, a q-gram variation of BNDM. As a result, we get several new variations of SBNDMq. In addition, we introduce a greedy skip loop for SBNDM2. We tune up our algorithms and the reference algorithms with 2-byte read. According to our experiments, the best of the new variations are faster than the winners of recent algorithm comparisons for English, DNA, and binary data.

A compact representation of nondeterministic (suffix) automata for the bit-parallel approach

We present a novel technique, suitable for bit-parallelism, for representing both the nondeterministic automaton and the nondeterministic suffix automaton of a given string in a more compact way. Our approach is based on a particular factorization of strings which on the average allows to pack in a machine word of w bits automata state configurations for strings of length greater than w. We adapted the Shift-And and BNDM algorithms using our encoding and compared them with the original algorithms. Experimental results show that the new variants are generally faster for long patterns.

EFFICIENT VARIANTS OF THE BACKWARD-ORACLE-MATCHING ALGORITHM

In this article we present two efficient variants of the BOM string matching algorithm which are more efficient and flexible than the original algorithm. We also present bit-parallel versions of them obtaining an efficient variant of the BNDM algorithm. Then we compare the newly presented algorithms with some of the most recent and effective string matching algorithms. It turns out that the new proposed variants are very flexible and achieve very good results, especially in the case of large alphabets.

Improving practical exact string matching

We present improved variations of the BNDM algorithm for exact string matching. At each alignment our bit-parallel algorithms process a q-gram before testing the state variable. In addition we apply reading a 2-gram in one instruction. Our point of view is practical efficiency of algorithms. Our experiments show that the new variations are faster than earlier algorithms in many cases.

On-line string matching algorithms: survey and experimental results

In this paper we present a short survey and experimental results for well known sequential string matching algorithms. We consider algorithms based on different approaches including classical, suffix automata, bit-parallelism and hashing. We put special emphasis on algorithms recently presented such as Shift-Or and BNDM algorithms. We compare these algorithms in terms of the number of character comparisons and the running time for four different types of text: binary alphabet, alphabet of size 8, English alphabet and DNA alphabet.