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Pure multiple RNA secondary structure alignments: a progressive profile approach
| Venue: | IEEE/ACM Trans. Comput. Biol. Bioinform |
| Citations: | 73 - 3 self |
BibTeX
@ARTICLE{Höchsmann_puremultiple,
author = {Matthias Höchsmann and Björn Voss and Robert Giegerich},
title = {Pure multiple RNA secondary structure alignments: a progressive profile approach},
journal = {IEEE/ACM Trans. Comput. Biol. Bioinform},
year = {},
pages = {2004}
}
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Abstract
Abstract—In functional, noncoding RNA, structure is often essential to function. While the full 3D structure is very difficult to determine, the 2D structure of an RNA molecule gives good clues to its 3D structure, and for molecules of moderate length, it can be predicted with good reliability. Structure comparison is, in analogy to sequence comparison, the essential technique to infer related function. We provide a method for computing multiple alignments of RNA secondary structures under the tree alignment model, which is suitable to cluster RNA molecules purely on the structural level, i.e., sequence similarity is not required. We give a systematic generalization of the profile alignment method from strings to trees and forests. We introduce a tree profile representation of RNA secondary structure alignments which allows reasonable scoring in structure comparison. Besides the technical aspects, an RNA profile is a useful data structure to represent multiple structures of RNA sequences. Moreover, we propose a visualization of RNA consensus structures that is enriched by the full sequence information. Index Terms—Alignment of trees, RNA secondary structures, noncoding RNAs.
Keyphrases
progressive profile approach rna molecule rna secondary structure structure comparison systematic generalization index term alignment rna sequence multiple structure good reliability rna profile rna consensus profile alignment method related function full sequence information noncoding rna sequence similarity multiple alignment rna secondary structure alignment technical aspect essential technique structural level useful data structure moderate length tree profile representation tree alignment model good clue
