A 3D pattern matching algorithm for DNA sequences | Zendy

Joan Hérisson | Zendy; Guillaume Payen | Zendy; Rachid Gherbi | Zendy

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A 3D pattern matching algorithm for DNA sequences

Author(s) -

Joan Hérisson,

Guillaume Payen,

Rachid Gherbi

Publication year - 2007

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btl669

Subject(s) - algorithm , dna , dna sequencing , computer science , matching (statistics) , representation (politics) , coding (social sciences) , construct (python library) , trajectory , computational biology , theoretical computer science , biology , mathematics , genetics , physics , political science , law , programming language , astronomy , statistics , politics

Biologists usually work with textual DNA sequences (succession of A, C, G and T). This representation allows biologists to study the syntax and other linguistic properties of DNA sequences. Nevertheless, such a linear coding offers only a local and a one-dimensional vision of the molecule. The 3D structure of DNA is known to be very important in many essential biological mechanisms. By using 3D conformation models, one is able to construct a 3D trajectory of a naked DNA molecule. From the various studies that we performed, it turned out that two very different textual DNA sequences could have similar 3D structures.

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