Journal ArticleDOI
Fast and practical approximate string matching
Reads0
Chats0
TLDR
This work presents an algorithm for string matching with mismatches based in arithmetical operations that runs in linear worst case time for most practical cases and presents a new approach to string searching.About:
This article is published in Information Processing Letters.The article was published on 1996-07-08. It has received 115 citations till now. The article focuses on the topics: String searching algorithm & Commentz-Walter algorithm.read more
Citations
More filters
Journal ArticleDOI
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
TL;DR: Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches and can be used simultaneously to achieve even greater alignment speeds.
Journal ArticleDOI
A guided tour to approximate string matching
TL;DR: This work surveys the current techniques to cope with the problem of string matching that allows errors, and focuses on online searching and mostly on edit distance, explaining the problem and its relevance, its statistical behavior, its history and current developments, and the central ideas of the algorithms.
Journal ArticleDOI
CloudBurst: highly sensitive read mapping with MapReduce
TL;DR: CloudBurst is a new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping and personal genomics.
Journal ArticleDOI
Using quality scores and longer reads improves accuracy of Solexa read mapping
TL;DR: The RMAP tool, which can map reads having a wide range of lengths and allows base-call quality scores to determine which positions in each read are more important when mapping, indicates that significant gains in Solexa read mapping performance can be achieved by considering the information in 3' ends of longer reads, and appropriately using the base- call quality scores.
Posted Content
Faster and More Accurate Sequence Alignment with SNAP
Matei Zaharia,William J. Bolosky,Kristal Curtis,Armando Fox,David A. Patterson,Scott Shenker,Ion Stoica,Richard M. Karp,Taylor Sittler +8 more
TL;DR: The Scalable Nucleotide Alignment Program is presented, a new short and long read aligner that is both more accurate and faster than state-of-the-art tools such as BWA and provides a rich error model that can match classes of mutations that today's fast aligners ignore.
References
More filters
Journal ArticleDOI
Efficient string matching: an aid to bibliographic search
TL;DR: A simple, efficient algorithm to locate all occurrences of any of a finite number of keywords in a string of text that has been used to improve the speed of a library bibliographic search program by a factor of 5 to 10.
Journal ArticleDOI
Fast Pattern Matching in Strings
TL;DR: 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.
Journal ArticleDOI
Fast text searching: allowing errors
Sun Wu,Udi Manber +1 more
TL;DR: 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.
Journal ArticleDOI
An O ( ND ) difference algorithm and its variations
TL;DR: A simpleO(ND) time and space algorithm is developed whereN is the sum of the lengths of A andB andD is the size of the minimum edit script forA andB, and the algorithm performs well when differences are small and is consequently fast in typical applications.
Journal ArticleDOI
A new approach to text searching
TL;DR: A family of simple and fast algorithms for solving the classical string matching problem, string matching with don't care symbols and complement symbols, and multiple patterns are introduced.