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Nucleic Acids Research 2006 34(Web Server issue):W696-W699; doi:10.1093/nar/gkl169
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© The Author 2006. Published by Oxford University Press. All rights reserved
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Article

SPRING: a tool for the analysis of genome rearrangement using reversals and block-interchanges

Ying Chih Lin, Chin Lung Lu1,*, Ying-Chuan Liu and Chuan Yi Tang

Department of Computer Science, National Tsing Hua University Hsinchu 300, Taiwan, ROC 1 Department of Biological Science and Technology, National Chiao Tung University Hsinchu 300, Taiwan, ROC

*To whom correspondence should be addressed. Tel: +886 3 5712121 ext. 56949; Fax: +886 3 5729288; Email: cllu{at}mail.nctu.edu.tw

Received February 14, 2006. Revised March 20, 2006. Accepted March 20, 2006.

SPRING (http://algorithm.cs.nthu.edu.tw/tools/SPRING/) is a tool for the analysis of genome rearrangement between two chromosomal genomes using reversals and/or block-interchanges. SPRING takes two or more chromosomes as its input and then computes a minimum series of reversals and/or block-interchanges between any two input chromosomes for transforming one chromosome into another. The input of SPRING can be either bacterial-size sequences or gene/landmark orders. If the input is a set of chromosomal sequences then the SPRING will automatically search for identical landmarks, which are homologous/conserved regions shared by all input sequences. In particular, SPRING also computes the breakpoint distance between any pair of two chromosomes, which can be used to compare with the rearrangement distance to confirm whether they are correlated or not. In addition, SPRING shows phylogenetic trees that are reconstructed based on the rearrangement and breakpoint distance matrixes.


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