Fast algorithms for approximate circular string matching

Barton, Carl; Iliopoulos, Costas S.; Pissis, Solon P.

doi:10.1186/1748-7188-9-9

Cited by 29 publications

(26 citation statements)

References 28 publications

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“…In [3], the authors have presented an approximate circular string matching with k-mismatches via filtering (ACSMF-Simple). They have built a library for ACSMF-Simple algorithm [3].…”

Section: Fast Ecpm Algorithmmentioning

confidence: 99%

See 1 more Smart Citation

A fast and lightweight filter-based algorithm for circular pattern matching

Azim

Iliopoulos

Rahman

et al. 2014

Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

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“…In [3], the authors have presented an approximate circular string matching with k-mismatches via filtering (ACSMF-Simple). They have built a library for ACSMF-Simple algorithm [3].…”

Section: Fast Ecpm Algorithmmentioning

confidence: 99%

“…The variations of approximate circular string [9] has also been considered in the literature. Very recently in [3], the authors have presented an average-case time O(n) algorithm for exact circular string matching where n is the length of the text T .…”

Section: Introductionmentioning

confidence: 99%

A fast and lightweight filter-based algorithm for circular pattern matching

Azim

Iliopoulos

Rahman

et al. 2014

Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

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“…To this end, alignment-free methods have been considered to speed-up the computation [35, 36]. The more general problem of searching for a circular pattern in a text under the edit distance model has also been studied extensively [37], and an average-case optimal algorithm is known [38]. …”

Section: Introductionmentioning

confidence: 99%

MARS: improving multiple circular sequence alignment using refined sequences

Ayad

Pissis

2017

BMC Genomics

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BackgroundA fundamental assumption of all widely-used multiple sequence alignment techniques is that the left- and right-most positions of the input sequences are relevant to the alignment. However, the position where a sequence starts or ends can be totally arbitrary due to a number of reasons: arbitrariness in the linearisation (sequencing) of a circular molecular structure; or inconsistencies introduced into sequence databases due to different linearisation standards. These scenarios are relevant, for instance, in the process of multiple sequence alignment of mitochondrial DNA, viroid, viral or other genomes, which have a circular molecular structure. A solution for these inconsistencies would be to identify a suitable rotation (cyclic shift) for each sequence; these refined sequences may in turn lead to improved multiple sequence alignments using the preferred multiple sequence alignment program.ResultsWe present MARS, a new heuristic method for improving Multiple circular sequence Alignment using Refined Sequences. MARS was implemented in the C++ programming language as a program to compute the rotations (cyclic shifts) required to best align a set of input sequences. Experimental results, using real and synthetic data, show that MARS improves the alignments, with respect to standard genetic measures and the inferred maximum-likelihood-based phylogenies, and outperforms state-of-the-art methods both in terms of accuracy and efficiency. Our results show, among others, that the average pairwise distance in the multiple sequence alignment of a dataset of widely-studied mitochondrial DNA sequences is reduced by around 5% when MARS is applied before a multiple sequence alignment is performed.ConclusionsAnalysing multiple sequences simultaneously is fundamental in biological research and multiple sequence alignment has been found to be a popular method for this task. Conventional alignment techniques cannot be used effectively when the position where sequences start is arbitrary. We present here a method, which can be used in conjunction with any multiple sequence alignment program, to address this problem effectively and efficiently.

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“…FLASM is well-suited to solving numerous problems in computational molecular biology, including, for instance, multiple circular sequence alignment (MCSA) [8] and motif extraction [9–11]. FLASM is also very useful for solving problems outside the confines of computational biology, such as approximate circular string matching [12] as well as implementing the Chang and Marr index [13]. A brief description of these applications follows below.…”

Section: Introductionmentioning

confidence: 99%

“…ACSM has various applications such as finding permutations in proteins [36], but it has other uses outside of biology and has been applied extensively in pattern recognition (see [37], for instance). Many average-case algorithms exist to tackle the ACSM problem efficiently for low error ratios k / m [12, 35, 38, 39]. …”

Section: Introductionmentioning

confidence: 99%

libFLASM: a software library for fixed-length approximate string matching

2016

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BackgroundApproximate string matching is the problem of finding all factors of a given text that are at a distance at most k from a given pattern. Fixed-length approximate string matching is the problem of finding all factors of a text of length n that are at a distance at most k from any factor of length ℓ of a pattern of length m. There exist bit-vector techniques to solve the fixed-length approximate string matching problem in time and space under the edit and Hamming distance models, where w is the size of the computer word; as such these techniques are independent of the distance threshold k or the alphabet size. Fixed-length approximate string matching is a generalisation of approximate string matching and, hence, has numerous direct applications in computational molecular biology and elsewhere.ResultsWe present and make available libFLASM, a free open-source C++ software library for solving fixed-length approximate string matching under both the edit and the Hamming distance models. Moreover we describe how fixed-length approximate string matching is applied to solve real problems by incorporating libFLASM into established applications for multiple circular sequence alignment as well as single and structured motif extraction. Specifically, we describe how it can be used to improve the accuracy of multiple circular sequence alignment in terms of the inferred likelihood-based phylogenies; and we also describe how it is used to efficiently find motifs in molecular sequences representing regulatory or functional regions. The comparison of the performance of the library to other algorithms show how it is competitive, especially with increasing distance thresholds.ConclusionsFixed-length approximate string matching is a generalisation of the classic approximate string matching problem. We present libFLASM, a free open-source C++ software library for solving fixed-length approximate string matching. The extensive experimental results presented here suggest that other applications could benefit from using libFLASM, and thus further maintenance and development of libFLASM is desirable.

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Fast algorithms for approximate circular string matching

Cited by 29 publications

References 28 publications

A fast and lightweight filter-based algorithm for circular pattern matching

A fast and lightweight filter-based algorithm for circular pattern matching

MARS: improving multiple circular sequence alignment using refined sequences

libFLASM: a software library for fixed-length approximate string matching

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