Detection and validation of single gene inversions

被引：45
作者：
Lefebvre, J. F. [2 ]
El-Mabrouk, N. [2 ]
Tillier, E. [3 ]
Sankoff, D. [1 ]
机构：
[1] Univ Ottawa, Dept Math & Stat, Ottawa, ON K1N 6N5, Canada
[2] Univ Montreal, Dept Informat & Rech Operat, Montreal, PQ H3C 3J7, Canada
[3] Princess Margaret Hosp, Ontario Canc Inst, Toronto, ON M4X 1K9, Canada
来源：
BIOINFORMATICS | 2003年 / 19卷
关键词：
short inversions; reversals; genome rearrangement; genome evolution; comparative genomics; bacterial genomes; Hannenhalli-Pevzner algorithm; experimental algorithmics;
D O I：
10.1093/bioinformatics/btg1025
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
Motivation: The biologically meaningful algorithmic study of genome rearrangement should take into account the distribution of sizes of the rearranged genomic fragments. In particular, it is important to know the prevalence of short inversions in order to understand the patterns of gene order disruption observed in comparative genomics. Results: We find a large excess of short inversions, especially those involving a single gene, in comparison with a random inversion model. This is demonstrated through comparison of four pairs of bacterial genomes, using a specially-designed implementation of the Hannenhalli-Pevzner theory, and validated through experimentation on pairs of random genomes matched to the real pairs.
引用
收藏
页码：i190 / i196
页数：7
相关论文
共 20 条
  • [1] Ajana Y, 2002, LECT NOTES COMPUT SC, V2452, P300
  • [2] BERGERON A, 2001, LECT NOTES COMPUTER, V2089, P106
  • [3] BERMAN P, 1996, LECT NOTES COMPUT SC, V1075, P168
  • [4] Blanchette M, 1996, GENE, V172, pGC11, DOI 10.1016/0378-1119(95)00878-0
  • [5] Measuring genome divergence in bacteria: A case study using Chlamydian data
    Dalevi, DA
    Eriksen, N
    Eriksson, K
    Andersson, SGE
    [J]. JOURNAL OF MOLECULAR EVOLUTION, 2002, 55 (01) : 24 - 36
  • [6] Hannenhalli S., 1995, Proceedings of the Twenty-Seventh Annual ACM Symposium on the Theory of Computing, P178, DOI 10.1145/225058.225112
  • [7] A faster and simpler algorithm for sorting signed permutations by reversals
    Kaplan, H
    Shamir, R
    Tarjan, RE
    [J]. SIAM JOURNAL ON COMPUTING, 2000, 29 (03) : 880 - 892
  • [8] McLysaght A, 2000, COMP GENOMICS, P47
  • [9] The lengths of undiscovered conserved segments in comparative maps
    Nadeau, JH
    Sankoff, D
    [J]. MAMMALIAN GENOME, 1998, 9 (06) : 491 - 495
  • [10] Segmental duplications and the evolution of the primate genome
    Samonte, RV
    Eichler, EE
    [J]. NATURE REVIEWS GENETICS, 2002, 3 (01) : 65 - 72
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