Local RNA structure alignment with incomplete sequence

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.