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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.<\/jats:p>","DOI":"10.1142\/s021972001000504x","type":"journal-article","created":{"date-parts":[[2010,8,23]],"date-time":"2010-08-23T04:04:28Z","timestamp":1282536268000},"page":"967-980","source":"Crossref","is-referenced-by-count":3,"title":["ON COMPARING TWO STRUCTURED RNA MULTIPLE ALIGNMENTS"],"prefix":"10.1142","volume":"08","author":[{"given":"VANDANABEN","family":"PATEL","sequence":"first","affiliation":[{"name":"Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey 07102, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"JASON T. 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