Related Experiment Video
Updated: Feb 13, 2026

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling
Published on: October 8, 2019
NeSSie: a tool for the identification of approximate DNA sequence symmetries
Michele Berselli1, Enrico Lavezzo1, Stefano Toppo1
1Department of Molecular Medicine, University of Padova, Padova, Italy.
Motivation:
Non-B DNA conformations play an important role in genomic rearrangements, structural three-dimensional organization and gene regulation. Many non-B DNA structures show symmetrical properties as palindromes and mirrors that can form hairpins, cruciform structures or triplexes. A comprehensive tool, capable to perform a fast genome wide search for exact and degenerate symmetrical patterns, is needed for further investigating nucleotide tracts potentially forming non-B DNA structures.
Results:
We developed NeSSie, an easily customizable C/C++ 64-bit library and tool, based on dynamic programming, to quickly scan for perfect and degenerate DNA palindromes, mirrors and potential triplex forming patterns. In addition, the tool computes linguistic complexity and Shannon entropy measures to verify the repetitive nature of the DNA regions enriched in these motifs. As a case study, the analysis of the Mycobacterium bovis genome is presented.
Availability And Implementation:
http://www.medcomp.medicina.unipd.it/main_site/doku.php? id=nessie and https://github.com/B3rse/nessie.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
More Related Videos
Related Concept Videos
Symmetry
Approximate Integration
Linearization and Approximation
Application of Linearization and Approximation
Accuracy, limits, and approximation
Accuracy is defined as the closeness of the measured value to the true or actual value. In engineering mechanics, repeated measurements are taken during theoretical or experimental analyses to ensure that the result is precise and accurate.
The accuracy of any solution is based on the...
Gauss's Law: Planar Symmetry

