A benchmark of multiple sequence alignment programs upon structural RNAs |
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| Authors: | Gardner Paul P Wilm Andreas Washietl Stefan |
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| Affiliation: | Department of Evolutionary Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark;1Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany;2Institut für Theoretische Chemie, Universität Wien, Währingerstrasse 17, A-1090 Wien, Austria |
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| Abstract: | To date, few attempts have been made to benchmark the 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. This work was aimed at achieving the following goals: (i) 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 and (ii) 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 <50–60% sequence identity. Second, we note that the probabilistic method ProAlign and the aging Clustal algorithms generally outperform other sequence-based algorithms, under the broadest range of applications. |
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