NR‐grep: a fast and flexible pattern‐matching tool

@article{Navarro2001NRgrepAF,
  title={NR‐grep: a fast and flexible pattern‐matching tool},
  author={Gonzalo Navarro},
  journal={Software: Practice and Experience},
  year={2001},
  volume={31}
}
  • G. Navarro
  • Published 30 October 2001
  • Computer Science
  • Software: Practice and Experience
We present nrgrep (‘non‐deterministic reverse grep’), a new pattern‐matching tool designed for efficient search of complex patterns. Unlike previous tools of the grep family, such as agrep and Gnu grep, nrgrep is based on a single and uniform concept: the bit‐parallel simulation of a non‐deterministic suffix automaton. As a result, nrgrep can find from simple patterns to regular expressions, exactly or allowing errors in the matches, with an efficiency that degrades smoothly as the complexity… Expand
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References

SHOWING 1-10 OF 38 REFERENCES
Fast and flexible string matching by combining bit-parallelism and suffix automata
TLDR
A new automaton to recognize suffixes of patterns with classes of characters is introduced, which seems very adequate for computational biology applications, since it is the fastest algorithm to search on DNA sequences and flexible searching is an important problem in that area. Expand
A Bit-Parallel Approach to Suffix Automata: Fast Extended String Matching
TLDR
A new algorithm for string matching called BNDM, which is the bit-parallel simulation of a known (but recent) algorithm called BDM, and which can be extended to handle classes of characters in the pattern and in the text, multiple patterns and to allow errors in thepattern or in thetext, combining simplicity, efficiency and flexibility. Expand
Faster Approximate String Matching
TLDR
The algorithm is based on the simulation of a nondeterministic finite automaton built from the pattern and using the text as input and it is shown that the algorithms are among the fastest for typical text searching, being the fastest in some cases. Expand
Compact DFA Representation for Fast Regular Expression Search
TLDR
This work presents a new technique to encode a deterministic finite automaton (DFA) using (m+1)(2m-1 +|Σ|) bits, where m is the number of characters (excluding operator symbols) in the regular expression and Σ is the alphabet. Expand
GLIMPSE: A Tool to Search Through Entire File Systems
TLDR
Glimpse is particularly designed for personal information, such as one's own file system, that should support many types of queries, flexible interaction, low overhead, and customization, All these are important features of glimpse. Expand
Fast Pattern Matching in Strings
TLDR
An algorithm is presented which finds all occurrences of one given string within another, in running time proportional to the sum of the lengths of the strings, showing that the set of concatenations of even palindromes, i.e., the language $\{\alpha \alpha ^R\}^*$, can be recognized in linear time. Expand
A fast bit-vector algorithm for approximate string matching based on dynamic programming
  • E. Myers
  • Mathematics, Computer Science
  • JACM
  • 1999
TLDR
An algorithm of comparable simplicity that requires only O(kn/w) time by virtue of computing a bit representation of the relocatable dynamic programming matrix for the approximate string matching problem, and is found to be more efficient than the previous results for many choices of k and small. Expand
From Regular Expressions to Deterministic Automata
TLDR
The main theorem allows an elegant algorithm to be refined into an efficient one based on ‘marking of’ regular expressions based on derivatives of regular expressions, which constructs an automaton for the marked expression. Expand
A fast string searching algorithm
TLDR
The algorithm has the unusual property that, in most cases, not all of the first <italic>i</italic) characters of a character string, “<italic>.” in another string, are inspected. Expand
Fast text searching: allowing errors
TLDR
T h e string-matching problem is a very c o m m o n problem; there are many extensions to t h i s problem; for example, it may be looking for a set of patterns, a pattern w i t h "wi ld cards," or a regular expression. Expand
...
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