A Parallel Solution to the Approximate String Matching Problem

Bertossi, Alan A.; Luccio, Fabrizio; Pagli, Linda; Lodi, Elena

doi:10.1093/comjnl/35.5.524

Cited by 3 publications

(4 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Alternative implementations and other optimisations should reduce running times in a production model. 7. Future developments SP21 is a software simulation which runs on a conventional computer.…”

Section: Resultsmentioning

confidence: 99%

“…D) for the basic dynamic programming method; the method appears to be better suited to parallel processing although, for the approximate string matching problem, an adaptation of dynamic programming for parallel processing has been described [7]; the technique for pruning the search tree may be applied, however large the search space may be. It appears that the technique may be generalised to related problems such as the N-lcs problem without the problems of computational complexity which arise with dynamic programming [22].…”

Section: Discussion Of the Search Techniquementioning

confidence: 99%

“…The dynamic programming method can be generalised to reveal the longest common sub-sequence between the two strings [31]. The method can also be generalised for the hcs problems [19] and for the approximate string matching problem [7].…”

Section: Previous Studiesmentioning

confidence: 99%

See 2 more Smart Citations

A scaleable technique for best-match retrieval of sequential information using metrics-guided search

Wolff

1994

Journal of Information Science

View full text Add to dashboard Cite

A new technique is described for retrieving information by finding the best match or matches between a textual 'query' and a textual database. The technique uses principles of beam search with a measure of probability to guide the search and prune the search tree. Unlike many methods for comparing strings, the method gives a set of alternative matches, graded by the 'quality' of the matching achieved.For any one sequence of hits between a query and a database, the probability measure is an estimate of the probability that the observed configuration, or better, could have occurred by chance. This probability is an inverse measure of the redundancy between the query and the database. The new technique is embodied in a software simulation called SP21 which runs on a conventional computer.Examples are presented showing best-match retrieval of information from a textual database.Analytic and empirical evidence is presented showing that, in a serial processing environment, the search technique has time complexity of O( Q : D ) where Q is the size of the query in characters and D is the size of the database in characters.The technique lends itself well to parallel processing. In that kind of environment, the time complexity of the process should approach O( Q ), depending on how well the parallelism is applied. The space complexity of the process is O( D ).Planned developments of these ideas in the future are described and discussed.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Discussion Of the Search Techniquementioning

confidence: 99%

See 1 more Smart Citation

A scaleable technique for best-match retrieval of sequential information using metrics-guided search

Wolff

1994

Journal of Information Science

View full text Add to dashboard Cite

show abstract

“…In this paper, we consider the fixed-length approximate string-matching with k-mismatches problem: given a text t, a pattern x and an integer ℓ, search for all the occurrences in t with k or fewer mismatches of all factors of x of length ℓ. There has been ample work in the literature for devising parallel algorithms for different models and platforms, for the approximate string-matching problem [2], [4], [6], [10], [13]. We design and analyse a practical parallel algorithm for addressing the fixed-length approximate string-matching problem with k-mismatches in O( nm⌈ℓ/w⌉ p ) time.…”

Section: Introductionmentioning

confidence: 99%

A Parallel Algorithm for Fixed-Length Approximate String-Matching with k-mismatches

Crochemore

Iliopoulos

Pissis

2010

Algorithms and Applications

View full text Add to dashboard Cite

This paper deals with the approximate string-matching problem with Hamming distance. The approximate string-matching with kmismatches problem is to find all locations at which a query of length m matches a factor of a text of length n with k or fewer mismatches. The approximate string-matching algorithms have both pleasing theoretical features, as well as direct applications, especially in computational biology. We consider a generalisation of this problem, the fixed-length approximate string-matching with k-mismatches problem: given a text t, a pattern x and an integer ℓ, search for all the occurrences in t of all factors of x of length ℓ with k or fewer mismatches with a factor of t. We present a practical parallel algorithm of comparable simplicity that requires only O(nm⌈ℓ/w⌉ p) time, where w is the word size of the machine (e.g. 32 or 64 in practice) and p the number of processors. Thus the algorithm's performance is independent of k and the alphabet size |Σ|. The proposed parallel algorithm makes use of message-passing parallelism model, and word-level parallelism for efficient approximate string-matching.

show abstract

Reconfigurable Parallel Approximate String Matching on FPGAs

Park

8th Euromicro Conference on Digital System Design (DSD'05)

View full text Add to dashboard Cite

A Parallel Solution to the Approximate String Matching Problem

Cited by 3 publications

References 0 publications

A scaleable technique for best-match retrieval of sequential information using metrics-guided search

A scaleable technique for best-match retrieval of sequential information using metrics-guided search

A Parallel Algorithm for Fixed-Length Approximate String-Matching with k-mismatches

Reconfigurable Parallel Approximate String Matching on FPGAs

Contact Info

Product

Resources

About