title: The RNA structure alignment ontology.
abstract: 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-dimensional (2D) matrices, with rows representing individual sequences, and columns identifying nucleotides from different sequences that correspond structurally, functionally, and/or evolutionarily. However, the requirement that sequences and structures correspond nucleotide-by-nucleotide is unrealistic and hinders representation of important biological relationships. High-throughput sequencing efforts are also rapidly making 2D alignments unmanageable because of vertical and horizontal expansion as more sequences are added. Solving the shortcomings of traditional RNA sequence alignments requires explicit annotation of the meaning of each relationship within the alignment. We introduce the notion of "correspondence," which is an equivalence relation between RNA elements in sets of sequences as the basis of an RNA alignment ontology. The purpose of this ontology is twofold: first, to enable the development of new representations of RNA data and of software tools that resolve the expansion problems with current RNA sequence alignments, and second, to facilitate the integration of sequence data with secondary and three-dimensional structural information, as well as other experimental information, to create simultaneously more accurate and more exploitable RNA alignments.
authors.forename: James W
authors.initials: JW
authors.lastname: Brown
authors.forename: Amanda
authors.initials: A
authors.lastname: Birmingham
authors.forename: Paul E
authors.initials: PE
authors.lastname: Griffiths
authors.forename: Fabrice
authors.initials: F
authors.lastname: Jossinet
authors.forename: Rym
authors.initials: R
authors.lastname: Kachouri-Lafond
authors.forename: Rob
authors.initials: R
authors.lastname: Knight
authors.forename: B Franz
authors.initials: BF
authors.lastname: Lang
authors.forename: Neocles
authors.initials: N
authors.lastname: Leontis
authors.forename: Gerhard
authors.initials: G
authors.lastname: Steger
authors.forename: Jesse
authors.initials: J
authors.lastname: Stombaugh
authors.forename: Eric
authors.initials: E
authors.lastname: Westhof
mesh_terms: D000818:Animals; D001483:Base Sequence; D006801:Humans; D008954:Models, Biological; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012313:RNA / Q000032:analysis* / Q000737:chemistry; D016415:Sequence Alignment / Q000379:methods* / Q000639:trends; D017423:Sequence Analysis, RNA / Q000379:methods; D012689:Sequence Homology, Nucleic Acid; D012984:Software
chemical_list: D012313:RNA