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

Ying Lin | Zendy; C. L. Lu | Zendy; Yucheng Liu | Zendy; Chuan Yi Tang | Zendy

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

Author(s) -

Ying Lin,

C. L. Lu,

Yucheng Liu,

Chuan Yi Tang

Publication year - 2006

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkl169

Subject(s) - biology , breakpoint , genome , spring (device) , chromosome , phylogenetic tree , genetics , block (permutation group theory) , chromosomal rearrangement , inverted repeat , gene rearrangement , gene , combinatorics , karyotype , mathematics , physics , thermodynamics

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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