Journal Article

Local RNA structure alignment with incomplete sequence

Diana L. Kolbe and Sean R. Eddy

in Bioinformatics

Volume 25, issue 10, pages 1236-1243
Published in print May 2009 | ISSN: 1367-4803
Published online March 2009 | e-ISSN: 1460-2059 | DOI:

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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


Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  6035 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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