An Index based Pattern Matching using Multithreading

NirmalaDevi, S.; Rajagopalan, Sridhar

doi:10.5120/7774-0857

Cited by 4 publications

(1 citation statement)

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“…It stores all the index values of all characters and checks the first character of the pattern, which character appears first in the pattern as the starting matching position. Literature [ 8 ] proposes to establish index structure in DNA and protein sequences, design a multithread matching model based on DNA sequence index, match sequences of multiple tasks simultaneously and has high efficiency in DNA matching accuracy. Literature [ 9 ] proposes a hash function based on Hash-q to eliminate conflicts, providing a perfect and efficient hash value generation method.…”

Section: Introductionmentioning

confidence: 99%

[Retracted] Gene Position Index Mutation Detection Algorithm Based on Feedback Fast Learning Neural Network

Zuo

Tang

et al. 2021

Computational Intelligence and Neuroscience

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In the detection of genome variation, the research on the internal correlation of reference genome is deepening; the detection of variation in genome sequence has become the focus of research, and it has also become an effective path to find new genes and new functional proteins. The targeted sequencing sequence is used to sequence the exon region of a specific gene in cancer gene detection, and the sequencing depth is relatively large. Traditional alignment algorithms will lose some sequences, which will lead to inaccurate mutation detection. This paper proposes a mutation detection algorithm based on feedback fast learning neural network position index. By establishing a position index relationship for ACGT in the DNA sequence, the subsequence is decomposed into the position relationship of different subsequences corresponding to the main sequence. The positional relationship of the subsequence in the main sequence is determined by the positional relationship. Analyzing SNP and InDel mutations, even structural mutations, through the position correlation of sequences has the advantages of high precision and easy implementation by personal computers. The feedback fast learning neural network is used to verify whether there is a linear relationship between two or more positions. Experimental results show that the mutation points detected by position index are more than those detected by Bcftools, Freebye, Vanscan2, and Gatk.

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Section: Introductionmentioning

confidence: 99%

[Retracted] Gene Position Index Mutation Detection Algorithm Based on Feedback Fast Learning Neural Network

Zuo

Tang

et al. 2021

Computational Intelligence and Neuroscience

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Analyzing Large-Scale DNA Sequences on Multi-core Architectures

Memeti

Pllana

2015

2015 IEEE 18th International Conference on Computational Science and Engineering

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Abstract-Rapid analysis of DNA sequences is important in preventing the evolution of different viruses and bacteria during an early phase, early diagnosis of genetic predispositions to certain diseases (cancer, cardiovascular diseases), and in DNA forensics. However, real-world DNA sequences may comprise several Gigabytes and the process of DNA analysis demands adequate computational resources to be completed within a reasonable time. In this paper we present a scalable approach for parallel DNA analysis that is based on Finite Automata, and which is suitable for analyzing very large DNA segments. We evaluate our approach for real-world DNA segments of mouse (2.7GB), cat (2.4GB), dog (2.4GB), chicken (1GB), human (3.2GB) and turkey (0.2GB). Experimental results on a dual-socket shared-memory system with 24 physical cores show speedups of up to 17.6×. Our approach is up to 3× faster than a patternbased parallel approach that uses the RE2 library.

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