Introduction

MOTIVATION: To recognize remote relationships between RNA molecules, one must be able to align structures without regard to sequence similarity. We have implemented a method, which is swift [O(n(2))], sensitive and tolerant of large gaps and insertions. Molecules are broken into overlapping fragments, which are characterized by their memberships in a probabilistic classification based on local geometry and H-bonding descriptors. This leads to a probabilistic similarity measure that is used in a conventional dynamic programming method. RESULTS: Examples are given of database searching, the detection of structural similarities, which would not be found using sequence based methods, and comparisons with a previously published approach. AVAILABILITY AND IMPLEMENTATION: Source code (C and perl) and binaries for linux are freely available at www.zbh.uni-hamburg.de/fries.

Publications

  1. Fast alignment and comparison of RNA structures.
    Cite this
    Wiegels T, Bienert S, Torda AE, 2013-03-01 - Bioinformatics (Oxford, England)

Credits

  1. Tim Wiegels
    Developer

  2. Stefan Bienert
    Developer

  3. Andrew E Torda
    Investigator

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Summary
AccessionBT000301
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC, Perl
User InterfaceTerminal Command Line
Download Count0
Submitted ByAndrew E Torda