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Bioinformatics Advance Access originally published online on March 20, 2009
Bioinformatics 2009 25(10):1236-1243; doi:10.1093/bioinformatics/btp154
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Local RNA structure alignment with incomplete sequence

Diana L. Kolbe and Sean R. Eddy *

HHMI Janelia Farm Research Campus, Ashburn VA 20147, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Accuracy of automated structural RNA alignment is improved by using models that consider not only primary sequence but also secondary structure information. However, current RNA structural alignment approaches tend to perform poorly on incomplete sequence fragments, such as single reads from metagenomic environmental surveys, because nucleotides that are expected to be base paired are missing.

Results: We present a local RNA structural alignment algorithm, trCYK, for aligning and scoring incomplete sequences under a model using primary sequence conservation and secondary structure information when possible. The trCYK algorithm improves alignment accuracy and coverage of sequence fragments of structural RNAs in simulated metagenomic shotgun datasets.

Availability: The source code for Infernal 1.0, which includes trCYK, is available at http://infernal.janelia.org

Contact: kolbed{at}janelia.hhmi.org; eddys{at}janelia.hhmi.org

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Ivo Hofacker

Received on November 20, 2008; revised on March 12, 2009; accepted on March 14, 2009

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