On comparing two structured RNA multiple alignments

Vandanaben Patel, Jason T.L. Wang, Shefali Setia, Anurag Verma, Charles D. Warden, Kaizhong Zhang

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)967-980
Number of pages14
JournalJournal of Bioinformatics and Computational Biology
Issue number6
StatePublished - Dec 2010
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications


  • Multiple sequence alignment
  • consensus structure
  • phylogenetic tree


Dive into the research topics of 'On comparing two structured RNA multiple alignments'. Together they form a unique fingerprint.

Cite this