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Related Experiment Video

Updated: Jun 27, 2025

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules
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Rotate: A command-line program to rotate circular DNA sequences to start at a given position or string.

Richard Durbin1, Bianca De Sanctis1, Moritz Blumer1

  • 1Department of Genetics, University of Cambridge, Cambridge, England, CB2 3EH, UK.

Wellcome Open Research
|April 29, 2024
PubMed
Summary
This summary is machine-generated.

This study introduces "rotate," a free, open-source tool for linearizing and rotating circular DNA sequences. It efficiently prepares genomic data for downstream analyses like alignment, overcoming limitations of existing software.

Keywords:
Geneticsbioinformaticscircular DNAmitochondrial DNAplastid DNA

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Circular DNA molecules, common in bacteria, viruses, and plastids, require linearization and rotation for downstream analyses.
  • Existing software for sequence manipulation often has limitations, including restricted input size, lack of custom anchor options, or commercial licensing.

Purpose of the Study:

  • To present "rotate," a novel, open-source command-line program for efficient sequence manipulation.
  • To provide a flexible tool for linearizing and rotating circular DNA sequences to a common start position.

Main Methods:

  • Developed "rotate" as a standalone C program with no external dependencies.
  • Implemented functionalities for rotating sequences to a custom anchor string with specified mismatches.
  • Enabled offsetting sequences to a desired position.

Main Results:

  • "rotate" successfully linearizes and rotates circular DNA sequences to a specified starting point.
  • The program is highly efficient, demonstrating linear scaling with input size.
  • Demonstrated rapid processing of over a thousand mitochondrial sequences in seconds.

Conclusions:

  • "rotate" offers a fast, flexible, and accessible solution for preparing circular DNA sequences for bioinformatics analyses.
  • The tool overcomes limitations of existing software, supporting custom anchor strings and custom offsets.
  • Facilitates downstream analyses such as sequence alignment by ensuring standardized sequence orientation.