Hypercomplex cross-correlation of DNA sequences

DOI10.1142/S0218339010003470zbMATH Open1404.92141arXiv1402.5341OpenAlexW3101810314WikidataQ56091338 ScholiaQ56091338MaRDI QIDQ4560370FDOQ4560370

Authors: Jian-Jun Shu, Yajing Li 

Publication date: 12 December 2018

Published in: Journal of Biological Systems (Search for Journal in Brave)

Abstract: A hypercomplex representation of DNA is proposed to facilitate comparing DNA sequences with fuzzy composition. With the hypercomplex number representation, the conventional sequence analysis method, such as, dot matrix analysis, dynamic programming, and cross-correlation method have been extended and improved to align DNA sequences with fuzzy composition. The hypercomplex dot matrix analysis can provide more control over the degree of alignment desired. A new scoring system has been proposed to accommodate the hypercomplex number representation of DNA and integrated with dynamic programming alignment method. By using hypercomplex cross-correlation, the match and mismatch alignment information between two aligned DNA sequences are separately stored in the resultant real part and imaginary parts respectively. The mismatch alignment information is very useful to refine consensus sequence based motif scanning.

Full work available at URL: https://arxiv.org/abs/1402.5341

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zbMATH Keywords

DNA alignmenthypercomplex representation

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Dynamic programming (90C39)

Cites Work

• Algorithms on Strings, Trees and Sequences

Cited In (7)

• Pairwise alignment of the DNA sequence using hypercomplex number representation
• Symbolic complexity for nucleotide sequences: a sign of the genome structure
• A new real structure-preserving quaternion QR algorithm
• New structure-preserving algorithms of Gauss-Seidel and successive over-relaxation iteration methods for quaternion linear systems
• Long- and short-range correlations in genome organization
• Identifying DNA motifs based on match and mismatch alignment information
• The role played by exons in genomic DNA sequence correlations

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