The RNA structure alignment ontology

LETTER TO THE EDITOR The RNA structure alignment ontology

Multiple sequence alignments are powerful tools for understanding the structures, functions, and evolutionary histories of linear biological macromolecules (DNA, RNA, and proteins), and for finding homologs in sequence databases. We address several ontological issues related to RNA sequence alignments that are informed by structure. Multiple sequence alignments are usually shown as two-dimensio...

RNA structure and structural alignment

The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data

Biomedical Ontologies are intended to integrate diverse biomedical data to enable intelligent datamining and facilitate translation of basic research into useful clinical knowledge. We present the first version of RNAO, an ontology for integrating RNA 3D structural, biochemical and sequence data. While each 3D data file depicts the structure of a specific molecule, such data have broader signif...

SRP-RNA sequence alignment and secondary structure.

The secondary structures of the RNAs from the signal recognition particle, termed SRP-RNA, were derived buy comparative analyses of an alignment of 39 sequences. The models are minimal in that only base pairs are included for which there is comparative evidence. The structures represent refinements of earlier versions and include a new short helix.

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 ar...