The bit parallel method has also been compared with the traditional aho corasick algorithms which consumes more time and memory. String matching, generally including exact string matching and regular expression matching is used in many applications. Approximate string matching is an old problem, with applications for example in spelling correction, bioinformatics and signal processing 7. Approximate multiple pattern string matching using bit. It refers in general to searching for substrings of a text that are within a prede. The main contribution of the thesis consists of new algorithms for approximate string matching with kmismatches based on the bit parallelism technique. Bitparallel approach to approximate string matching in. The same idea can be used to boost other bitparallel algorithms such as multibdm navarro and ra. These algorithms are faster than the bitparallel ones, as they are simple and skip text characters.
Bitparallel approximate string matching under hamming. Bitparallel approximate string matching algorithms with transposition heikki hyyr. F 1 introduction the problem of string matching is to. Compression and bitparallelism techniques in selected. B denote the edit distance between the strings a and b, and k be the maximum allowed distance. Bit parallelism is the most important techniques in the field of computer science. We begin this paper by deriving a practically equivalent version of the algorithm of myers. In computer science, stringsearching algorithms, sometimes called stringmatching algorithms, are an important class of string algorithms that try to find a place where one or several strings also called patterns are found within a larger string or text a basic example of string searching is when the pattern and the searched text are arrays of elements of an alphabet. After shift or in 1998 navarro and raffinot were introduced new bit parallel algorithm named as bndm backward non deterministic matching 25. Bit parallel string matching under hamming distance in onmw worst case time. Then the task of approximate string matching is to. Efficient string matching using bit parallelism core. Bit parallel string matching alina gutnova june 21, 2006 1 introduction the string matching problem smp consists of. Here aab denotes the substring of a that begins at its ath character and ends at its bth character, for a b.
Speedingup the string matching algorithm will therefore result in accelerating the searching process in dna and binary data. Our algorithm can search for r patterns of any length in average time o. There are a variety of important bit parallel string matching algorithms exist like shiftor, bndm, tndm, sbndm, bndmq, shiftor with qgram, and multiple patterns bndm. Bitparallel multiple approximate string matching based on. Bitparallel approximate string matching under hamming distance. We consider bitparallel algorithms of boyermoore type for exact string matching. Then the above mentioned bpsm algorithm is described more carefully in the third section and some empirical results are given in the forth section. These algorithms are faster than the bit parallel ones, as they are simple and skip text characters. Bitparallel approximate string matching algorithms with. String matching searching string matchingorsearchingalgorithms try to nd places where one or several strings also called patterns are found within a larger string searched text try to find places where one or several strings also.
The main contribution of the thesis consists of new algorithms for approximate string matching with kmismatches based on the bitparallelism technique. Bitparallel algorithms are based on taking advantage of the fact that a single computer instruction manipulates bitvectors with w bits typically w 32 or 64 in the current computers. For understanding the functional requirements of string matching algorithms, we surveyed the real time parallel string matching patterns to handle the current trends. Index terms string matching, ahocorasick, commentz walter, bit parallel, rabinkarp, wumanber, fsm. This technique permits searching for the approximate occurrences of a pattern of length m in a text of length n in time o. The bitparallel technique was successfully applied in stringology especially for multiple pattern matching, approximate pattern matching and indexing. In recent years string matching plays a functional role in many application like information retrieval, gene analysis, pattern recognition, linguistics, bioinformatics etc. There are two ways of transforming a string of characters into a string. In the experiments, the presented algorithm outperforms earlier filtering methods with orders of magnitude faster search performance, especially for short. Bitparallel string matching under hamming distance in onmw worst case time.
Although this is asymptotically the optimal speedup over the basic omn time. Increased bitparallelism for approximate string matching. Using bitparallelism has resulted in fast and practical algorithms for approximate string matching under the levenshtein edit. Alternative algorithms for bit parallel string matching hannu peltola and jorma tarhio department of computer science and engineering helsinki university of technology p. We also developed a multiple matching for a 529 kefu xu et al. Vivek sharma tit college, bhopal, madhya pradesh, india abstract. A bit parallel algorithm is presented for online approximate matching of circular strings with k mismatches, which is the first averageoptimal solution that is not based on filtering. Index termsstring matching, bitparallel algorithm, inclusive scan, shiftor algorithm, wumanber algorithm, gpu. A recent development uses deterministic suffix automata to design new optimal string matching algorithms, e.
The shiftor algorithm for exact pattern matching 2 is one of the rst algorithms using this paradigm. A parallel automaton string matching with prehashing and. Pdf bitparallel string matching under hamming distance. Nested counters in bitparallel string matching springerlink. Since 1992, this bit parallelism is directly used in. For example, the wu and manber algorithm 12 nds approximate matches to a pattern.
When using qgrams we process q characters as a single character. Bndm, instead, sim ulates the nondeterministi c v ersion using bitparallel i sm. In the second section of the article we describe brie. Bitparallelism permits executing several operations simultaneously over a set of bits or numbers stored in a single computer word. The proposed algorithm shiftandtrajmatch is an extension of a bitparallel string matching algorithm called shiftand 2,6 on 2dimensional trajectory matching. The bndm algorithm itself has been developed from the backward dawg matching bdm algorithm 3.
Conclusion in this paper, we have proposed a bitparallel multiple approximate string match algorithm, and it performs better than the existing algorithm when the patterns are short. Bitparallel witnesses and their applications to approximate. Myers 1999 a fast bitvector algorithm for approximate string. The string matching problem smp consists of finding substring generally pattern p in text t. Bitparallel counters hierarchical bitparallel veri. Procedia computer science 17 20 523 a 529 gpu that is based on the modified algorithm. Bitparallel, pattern, qgram, string matching 1 introduction string matching 1,12 is a classical problem of computer science. Explaining and extending the bitparallel approximate. Previously, there are two types of fast algorithms exist, bitparallel. If many dataitems of an algorithm can be encoded into w bits, it may be possible to process many dataitems within a single instruction thus the name bitparallelism and achieve gain in time andor space. Bitparallel approximate string matching algorithms with transposition heikki hyyro1 department of computer sciences, university of tampere, finland available online 16 september 2004 abstract using bitparallelism has resulted in fast and practical algorithms for approximate string matching. Shift or algorithm shift or algorithm is an approximate multiple pattern.
Bitparallel search algorithms for long patterns helda university. We introduce a twoway modification of the bndm algorithm. Fast and flexible string matching by combining bit. The bit parallel approximate string matching algorithm of wu and manber is based on representing a nondeterministic finite automaton nfa by using bit vectors. Bitparallel algorithms have also been developed for the approximate string matching problem in which a pattern and text are given and occurrences of the pattern with at most kdi erences are sought in the text,12,2,9.
Stricter matching condition for any and the smallest that permits shifting the window is never smaller than for the basic method. Finite automata are very useful building blocks in. Pdf we consider bitparallel algorithms of boyermoore type for exact string matching. Although this is asymptotically the optimal bitparallel speedup over the.
Improved single and multiple approximate string matching kimmo fredriksson department of computer science, university of joensuu, finland. In general bit parallel are both memory and time efficient. It implements a bitparallel simulation of a nondeterministic automaton. Evolution of bit parallel algorithm this paper gives the detailed description of above bit parallel string matching algorithms. Increased bitparallelism for approximate and multiple. Bitparallel multiple pattern matching 3 these algorithms divide the complexity by w, where wis the length of a machine word. Navarro and raffinot 2002 flexible pattern matching in strings, sections 2. Next, in section 4, we introduce two new variations. A bitparallel, general integerscoring sequence alignment. We consider bit parallel algorithms of boyermoore type for exact string matching.
Bdm skips c haracters using a \su x automaton whic h is made deterministic in the prepro cessing. Introduction string matching is a technique to find out pattern from given text. A basic example of string searching is when the pattern and the searched text are arrays. Increased bitparallelism for approximate and multiple string. The extension is done by checking the condition on each candidate that matches the pattern. Three of our algorithms are based on the backward nondeterministic dawg matching bndm algorithm by navarro and ra. The algorithm, called bndm, is the bitparallel sim ulation of a kno wn but recen t algorithm called bdm. Improved single and multiple approximate string matching.
Bit parallelism is an inherent property of computer to perform bitwise a parallel operation on computer word, but it is performed only on data available in single computer word. Alternative algorithms for bitparallel string matching hannu peltola and jorma tarhio department of computer science and engineering helsinki university of technology p. The recently presented technique of nested counters matryoshka. Paper starts from very first algorithm based on bit parallelism up to latest one. The algorithm for multiple pattern matching mag allows to search in both compressed byte codes and plain text, achieving better results than its competitors in most analyzed cases. The idea behind using qgrams is to make the alphabet larger. This technique has yielded the fastest approximate string matching algorithms if we exclude.
Pdf nested counters in bitparallel string matching. Trajectory pattern matching based on bitparallelism for. Alternative algorithms for bitparallel string matching. Since 1992 bit parallelism is being used in string matching applications to improve the matching pace. Finally, we ran experiments on the real world trajectory data to evaluate the ef.
A bitparallel algorithm is presented for online approximate matching of circular strings with k mismatches, which is the first averageoptimal solution that is not based on filtering. Siam journal on computing society for industrial and. String matching problems with parallel approaches an. Efficient string matching using bit parallelism kapil kumar soni, rohit vyas, dr. Most classical string matching algorithms are aimed at quickly finding an exact pattern in a text, being knuthmorrispratt kmp and the boyermoore bm family the most famous ones. The results showed good performance enough for real applications. Pdf we explore the benefits of parallelizing 7 stateoftheart string. In the basic form both p and t consist of characters in the same alphabet s.
These algorithms are tunedboyermoore, skipsearch and maximalshift, each of which has a counterpart in exact string matching. In the matching phase a result bitvector ris iteratively andcombined with the. String matching is often used in different areas such as text editors, virus scanning, bioinformatics, digital libraries and web search engines. Bit parallel algorithms have also been developed for the approximate string matching problem in which a pattern and text are given and occurrences of the pattern with at most kdi erences are sought in the text,12,2,9. Gonzalo navarro abstract we present a new bitparallel technique for approximate string matching. Introduction string matching consists in finding one or more. Approximate string matching, also called string matching allowing errors, is the problem of finding a pattern p in a text t when a limited number k of differences is permitted between the pattern and its occurrences in the text. It was faster than the previous algorithms but gives false matches. The dynamic programming 6 and bit parallel 7 are inappropriate for long and multiple patterns, and the filtering. If the text character aligned with the end of the pattern is a mismatch, we continue by examining text characters after the alignment. Keywords approximate string matching, bit parallelism, shift or string matching. Explaining and extending the bitparallel approximate string. Faster bitparallel approximate string matching dcc uchile. We present a new bitparallel technique for approximate string matching.
A recent development uses deterministic suffix automata to design new optimal. In algorithm 1, we present the proposed trajectory matching. This was an exact single pattern string matching algorithm. In computer science, string searching algorithms, sometimes called string matching algorithms, are an important class of string algorithms that try to find a place where one or several strings also called patterns are found within a larger string or text.
This thesis considers the approximate matching problem known as string matching with kmismatches, in which kcharacters are allowed to mismatch. Our experimental results show that the result is competitive against. Approximate string matching rowwise bitparallelism. Bit parallelism is an inherent property of computer to perform bitwise a parallel operation on computer word, but it. Pdf alternative algorithms for bitparallel string matching. The intrinsic parallelism in bit operations like andor inside a computer word is known as bit parallelism. Bitparallelism is the technique of packing several values in a single computer word and updating them all in a single operation. Bitparallel witnesses and their applications to approximate string matching heikki hyyr.