SBARS: fast creation of dotplots for DNA sequences on different scales using GA-,GC-content | Zendy

Maxim Pyatkov | Zendy; A. N. Pankratov | Zendy

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SBARS: fast creation of dotplots for DNA sequences on different scales using GA-,GC-content

Author(s) -

Maxim Pyatkov,

A. N. Pankratov

Publication year - 2014

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/btu095

Subject(s) - gc content , content (measure theory) , dna , computer science , computational biology , biology , genetics , mathematics , gene , genome , mathematical analysis

Structural analysis of long DNA fragments, including chromosomes and whole genomes, is one of the main challenges in modern bioinformatics. Here, we propose an original approach based on spectral methods and its implementation called SBARS (Spectral-Based Approach for Repeats Search. The main idea of our approach is that repeated DNA structures are recognized not within the nucleotide sequence directly but within the function derived from this sequence. This allows us to investigate nucleotide sequences on different scales and decrease time complexity for dotplot creation down to [Formula: see text].

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