On comparing two structured RNA multiple alignments

Document Type

Article

Publication Date

12-1-2010

Abstract

We present a method, called BlockMatch, for aligning two blocks, where a block is an RNA multiple sequence alignment with the consensus secondary structure of the alignment in Stockholm format. The method employs a quadratic-time dynamic programming algorithm for aligning columns and column pairs of the multiple alignments in the blocks. Unlike many other tools that can perform pairwise alignment of either single sequences or structures only, BlockMatch takes into account the characteristics of all the sequences in the blocks along with their consensus structures during the alignment process, thus being able to achieve a high-quality alignment result. We apply BlockMatch to phylogeny reconstruction on a set of 5S rRNA sequences taken from fifteen bacteria species. Experimental results showed that the phylogenetic tree generated by our method is more accurate than the tree constructed based on the widely used ClustalW tool. The BlockMatch algorithm is implemented into a web server, accessible at . A jar file of the program is also available for download from the web server. © 2010 Imperial College Press.

Identifier

78649875667 (Scopus)

Publication Title

Journal of Bioinformatics and Computational Biology

External Full Text Location

https://doi.org/10.1142/S021972001000504X

ISSN

02197200

PubMed ID

21121021

First Page

967

Last Page

980

Issue

6

Volume

8

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