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

Authors: Frenkel-Morgenstern, Milana; Singer, Alice; Bronfeld, Hagit; Pietrokovski, Shmuel

Source: Nucleic Acids Research, Volume 33, Supplement 1, 1 July 2005 , pp. W281-W283(3)

Publisher: Oxford University Press

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Abstract:

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.

Document Type: Research article

DOI: http://dx.doi.org/10.1093/nar/gki488

Publication date: 2005-07-01

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Nucleic Acids Research (NAR) is a fully Open Access journal, providing rapid publication of leading edge research into the nucleic acids under the following categories: chemistry, computational biology, genomics, molecular biology, nucleic acid enzymes, RNA and structural biology. There is a Survey and Summary section, and methods papers are published
in NAR Methods Online. Each year the first issue is devoted to biological databases, and a later issue to relevant web-based software resources.