TBI-Preprint 05-04-001

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Titel:
A benchmark of multiple sequence alignment programs upon structural RNAs

Author(s):
Paul P. Gardner, Andreas Wilm, Stefan Washietl

appeared in:
Nucleic Acids Res. 33(8):2433-2439

Full text available free of charge: http://nar.oupjournals.org/cgi/content/full/33/8/2433

Abstract:
To date, few attempts have been made to benchmark alignment algorithms upon nucleic acid sequences. Frequently, sophisticated PAM or BLOSUM like models are used to align proteins, yet equivalents are not considered for nucleic acids; Instead, rather ad hoc models are generally favoured. Here we systematically test the performance of existing alignment algorithms on structural RNAs. The goals of this work are: (1) To determine conditions where it is appropriate to apply common sequence alignment methods to the structural RNA alignment problem. This indicates where and when researchers should consider augmenting the alignment process with auxiliary information, such as secondary structure. (2) To determine which sequence alignment algorithms perform well under the broadest range of conditions. We find that sequence alignment alone, using the current algorithms, is generally inappropriate below 50-60% sequence-identity, secondly we note that the probabilistic method ProAlign and the aging Clustal algorithms generally out-perform other sequence-based algorithms, under the broadest range of applications.