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

Maxim I Pyatkov; Anton N Pankratov

doi:10.1093/bioinformatics/btu095

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

Bioinformatics. 2014 Jun 15;30(12):1765-6. doi: 10.1093/bioinformatics/btu095. Epub 2014 Feb 14.

Authors

Maxim I Pyatkov¹, Anton N Pankratov¹

Affiliation

¹ Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow region 142290, Russia.

PMID: 24532721
DOI: 10.1093/bioinformatics/btu095

Abstract

Summary: 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].

Availability and implementation: Pre-compiled versions for Windows and Linux and documentation are available at http://mpyatkov.github.com/sbars/.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Base Composition
DNA / chemistry*
Genomics / methods
Repetitive Sequences, Nucleic Acid*
Sequence Analysis, DNA / methods*
Software*
Tandem Repeat Sequences

Substances

DNA