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Nucleic Acids Research 2005 33(Web Server Issue):W281-W283; doi:10.1093/nar/gki488
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

One-Block CYRCA: an automated procedure for identifying multiple-block alignments from single block queries

Milana Frenkel-Morgenstern, Alice Singer1, Hagit Bronfeld1 and Shmuel Pietrokovski*

Department of Molecular Genetics, Weizmann Institute of Science Rehovot 76100, Israel 1Bioinformatics undergraduate program, Bar-Ilan University Ramat-Gan 52900, Israel

*To whom correspondence should be addressed. Tel: +972 8 934 2747; Fax: +972 8 934 4108; Email: shmuel.pietrokovski{at}weizmann.ac.il

Received February 14, 2005. Revised March 3, 2005. Accepted April 20, 2005.

One-Block CYRCA is an automated procedure for identifying multiple-block alignments from single block queries (http://bioinfo.weizmann.ac.il/blocks/OneCYRCA). It is based on the LAMA and CYRCA block-to-block alignment methods. The procedure identifies whether the query blocks can form new multiple-block alignments (block sets) with blocks from a database or join pre-existing database block sets. Using pre-computed LAMA block alignments and CYRCA sets from the Blocks database reduces the computation time. LAMA and CYRCA are highly sensitive and selective methods that can augment many other sequence analysis approaches.


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