A benchmark of multiple sequence alignment programs upon structural RNAs

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...

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Published in:Nucleic acids research 2005-01, Vol.33 (8), p.2433-2439
Main Authors: Gardner, Paul P., Wilm, Andreas, Washietl, Stefan
Format: Article
Language:English
Subjects:
Algorithms
Nucleic Acid Conformation
Reproducibility of Results
RNA - chemistry
RNA, Untranslated - chemistry
Sequence Alignment - methods
Sequence Analysis, RNA - methods
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Wilm, Andreas
Washietl, Stefan
description 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
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subjects Algorithms
Nucleic Acid Conformation
Reproducibility of Results
RNA - chemistry
RNA, Untranslated - chemistry
Sequence Alignment - methods
Sequence Analysis, RNA - methods
title A benchmark of multiple sequence alignment programs upon structural RNAs
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