Pure multiple RNA secondary structure alignments: a progressive profile approach.

Matthias Höchsmann; Björn Voss; Robert Giegerich

doi:10.1109/tcbb.2004.11

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Pure multiple RNA secondary structure alignments: a progressive profile approach.

Matthias Höchsmann·Björn Voss·Robert Giegerich

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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.

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5' Untranslated Regions Algorithms Animals Base Sequence Computational Biology Ferritins Humans Mice Models, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA RNA, Transfer Sequence Alignment Sequence Homology, Nucleic Acid Journal Article

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Matthias Höchsmann, Björn Voss, Robert Giegerich. Pure multiple RNA secondary structure alignments: a progressive profile approach.. https://doi.org/10.1109/tcbb.2004.11

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