Processing Repetitive Sequence Structures with Mismatches at Streaming Rate

Conti, Albert A.; Court, Tom Van; Herbordt, Martin C.

doi:10.1007/978-3-540-30117-2_131

Cited by 5 publications

(2 citation statements)

References 3 publications

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“…DNA sequence is a string containing characters A, C, G and T, which means that Σ = {A, T, C, G} for DNA; Σ = {A,C,G,U} for RNA, and for the protein sequence, Σ = { A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y}. As stated in [19]: The development of fast methods for sequencing genes and proteins is one of the most significant technological achievements of recent times. This has enabled the creation of large databases which can be processed by abstracting sequences of nucleic acids (DNA, RNA) and amino acids (proteins) into strings of characters.…”

Section: Biological Sequencementioning

confidence: 99%

Efficient Algorithm for Extracting Complete Repeats from Biological Sequences

Yusufu¹,

Yusufu²

2015

IJCA

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In this paper, an approach for efficiently extracting the repeating patterns in a biological sequence is proposed. A repeating pattern is a subsequence which appears more than once in a sequence, which is one of the most important features that can be used for revealing functional or evolutionary relationships in biological sequences. The algorithm does a rapid scan of the string to find repeating regions where the repeating substring has been marked using length, occurrence positions, and occurrence frequency. The algorithm execute in linear time and space independent of alphabet size. The algorithm also has the capability to restrict output complete repeats in which length (period) p ≥ p min , where p min ≥ 1 is a user-specified minimum. The algorithm outputs complete repeats, and can be extended or applied to other situations, for example computing maximal repeats, or finding common motifs in a set of biological sequences.

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Section: Biological Sequencementioning

confidence: 99%

Efficient Algorithm for Extracting Complete Repeats from Biological Sequences

Yusufu¹,

Yusufu²

2015

IJCA

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“…The most important include string matching [1], approximate palindrome detection, repetitive structure detection [2] etc. The FPGA technology turned out to be more than appropriate for this kind of tasks.…”

Section: Introductionmentioning

confidence: 99%

Architecture model for approximate tandem repeat detection

Martínek

Lexa

2011

ASAP 2011 - 22nd IEEE International Conference on Application-Specific Systems, Architectures and Processors

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Algorithms for biological sequence analysis, such as approximate string matching or algorithms for identification of sequence patterns supporting specific structural elements, present good opportunities for hardware acceleration. Implementation of these algorithms often results in architectures based on multidimensional arrays of computing elements. Mapping effectively these computational structures on FPGAs remains one of the challenging problems. This paper focuses on a specific hardware architecture for detection of approximate tandem repeats in sequences. We show how to create a parametrized architecture model combined with an automatic technique that can determine appropriate circuit dimensions with respect to input task parameters and the target platform properties.

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