Publications
2009
Brown J W, Birmingham A, Griffiths P E, Jossinet F, Kachouri-Lafond R, Knight R, Lang B F, Leontis N, Steger G, Stombaugh J, Westhof E
The RNA structure alignment ontology Journal Article
In: RNA, vol. 15, no. 9, pp. 1623-1631, 2009, ISSN: 1469-9001 (Electronic) 1355-8382 (Linking), (Brown, James W Birmingham, Amanda Griffiths, Paul E Jossinet, Fabrice Kachouri-Lafond, Rym Knight, Rob Lang, B Franz Leontis, Neocles Steger, Gerhard Stombaugh, Jesse Westhof, Eric Letter Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. United States RNA (New York, N.Y.) RNA. 2009 Sep;15(9):1623-31. Epub 2009 Jul 21.).
Abstract | Links | BibTeX | Tags: Animals Base Sequence Humans Models, Biological Molecular Sequence Data Nucleic Acid Conformation Phylogeny RNA/*analysis/chemistry Sequence Alignment/*methods/trends Sequence Analysis, Nucleic Acid *Software, RNA/methods Sequence Homology, Unité ARN, WESTHOF
@article{,
title = {The RNA structure alignment ontology},
author = {J W Brown and A Birmingham and P E Griffiths and F Jossinet and R Kachouri-Lafond and R Knight and B F Lang and N Leontis and G Steger and J Stombaugh and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19622678},
doi = {rna.1601409 [pii] 10.1261/rna.1601409},
issn = {1469-9001 (Electronic) 1355-8382 (Linking)},
year = {2009},
date = {2009-01-01},
journal = {RNA},
volume = {15},
number = {9},
pages = {1623-1631},
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.},
note = {Brown, James W
Birmingham, Amanda
Griffiths, Paul E
Jossinet, Fabrice
Kachouri-Lafond, Rym
Knight, Rob
Lang, B Franz
Leontis, Neocles
Steger, Gerhard
Stombaugh, Jesse
Westhof, Eric
Letter
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
United States
RNA (New York, N.Y.)
RNA. 2009 Sep;15(9):1623-31. Epub 2009 Jul 21.},
keywords = {Animals Base Sequence Humans Models, Biological Molecular Sequence Data Nucleic Acid Conformation Phylogeny RNA/*analysis/chemistry Sequence Alignment/*methods/trends Sequence Analysis, Nucleic Acid *Software, RNA/methods Sequence Homology, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}