1. Local RNA structure alignment with incomplete sequence
- Author
-
Diana L. Kolbe and Sean R. Eddy
- Subjects
Statistics and Probability ,Models, Molecular ,Sequence analysis ,Structural alignment ,Sequence alignment ,Computational biology ,Biology ,computer.software_genre ,Biochemistry ,Databases, Genetic ,Consensus sequence ,Nucleic acid structure ,Molecular Biology ,Alignment-free sequence analysis ,Sequence (medicine) ,Multiple sequence alignment ,Sequence Analysis, RNA ,Original Papers ,Computer Science Applications ,Computational Mathematics ,Computational Theory and Mathematics ,Nucleic Acid Conformation ,RNA ,Data mining ,computer ,Sequence Analysis ,Sequence Alignment ,Algorithms - 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@janelia.hhmi.org; eddys@janelia.hhmi.org Supplementary information: Supplementary data are available at Bioinformatics online.
- Published
- 2009