BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btt006 Structural bioinformatics Advance Access publication January 12, 2013 Fast alignment and comparison of RNA structures (2012)
BibTeX
@MISC{Wiegels12bioinformaticsoriginal,
author = {Tim Wiegels and Stefan Bienert and Andrew E. Torda},
title = {BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btt006 Structural bioinformatics Advance Access publication January 12, 2013 Fast alignment and comparison of RNA structures},
year = {2012}
}
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Abstract
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(n2)], 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 program-ming 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 bin-aries for linux are freely available at www.zbh.uni-hamburg.de/fries. Contact:
