SPRING: a tool for the analysis of genome rearrangement using reversals and block-interchanges.
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.
Lin
Ying Chih
YC
Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC.
Lu
Chin Lung
CL
Liu
Ying-Chuan
YC
Tang
Chuan Yi
CY
D007446:Chromosome Inversion; D002875:Chromosomes; D002876:Chromosomes, Bacterial; D020563:Gammaproteobacteria / Q000235:genetics; D023061:Gene Order; D015321:Gene Rearrangement; D023281:Genomics / Q000379:methods*; D020407:Internet; D010802:Phylogeny; D011995:Recombination, Genetic; D012984:Software; D014584:User-Computer Interface; D014733:Vibrio / Q000235:genetics