CREx: inferring genomic rearrangements based on common intervals

被引：266
作者：
Bernt, Matthias [1 ]
Merkle, Daniel
Ramsch, Kai
Fritzsch, Guido
Perseke, Marleen
Bernhard, Detlef
Schlegel, Martin
Stadler, Peter F.
Middendorf, Martin
机构：
[1] Univ Leipzig, Parallel Comp & Complex Syst Grp, Leipzig, Germany
[2] Univ Leipzig, Bioinformat Grp, Dept Comp Sci, Leipzig, Germany
[3] Univ Leipzig, Interdisciplinary Ctr Bioinformat, Leipzig, Germany
[4] Univ Leipzig, Inst Biol 2, Leipzig, Germany
[5] Fraunhofer Inst IZI, Leipzig, Germany
[6] Univ Vienna, Dept Theoret Chem, A-1010 Vienna, Austria
[7] Santa Fe Inst, Santa Fe, NM 87501 USA
来源：
BIOINFORMATICS | 2007年 / 23卷 / 21期
关键词：
D O I：
10.1093/bioinformatics/btm468
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
Summary: We present the web-based program CREx for heuristically determining pairwise rearrangement events in unichromosomal genomes. CREx considers transpositions, reverse transpositions, reversals and tandem-duplication-random-loss (TDRL) events. It supports the user in finding parsimonious rearrangement scenarios given a phylogenetic hypothesis. CREx is based on common intervals, which reflect genes that appear consecutively in several of the input gene orders.
引用
收藏
页码：2957 / 2958
页数：2
相关论文
共 12 条
  • [1] Mitochondrial gene rearrangement in the sea cucumber genus Cucumaria
    Arndt, A
    Smith, MJ
    [J]. MOLECULAR BIOLOGY AND EVOLUTION, 1998, 15 (08) : 1009 - 1016
  • [2] Perfect sorting by reversals is not always difficult
    Berard, Severine
    Bergeron, Anne
    Chauve, Cedric
    Paul, Christophe
    [J]. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2007, 4 (01) : 4 - 16
  • [3] On the similarity of sets of permutations and its applications to genome comparison
    Bergeron, Anne
    Stoye, Jens
    [J]. JOURNAL OF COMPUTATIONAL BIOLOGY, 2006, 13 (07) : 1340 - 1354
  • [4] Using median sets for inferring phylogenetic trees
    Bernt, Matthias
    Merkle, Daniel
    Middendorf, Martin
    [J]. BIOINFORMATICS, 2007, 23 (02) : E129 - E135
  • [5] Bernt M, 2007, LECT N BIOINFORMAT, V4463, P305
  • [6] Animal mitochondrial genomes
    Boore, JL
    [J]. NUCLEIC ACIDS RESEARCH, 1999, 27 (08) : 1767 - 1780
  • [7] TESTING FOR CONSECUTIVE ONES PROPERTY, INTERVAL GRAPHS, AND GRAPH PLANARITY USING PQ-TREE ALGORITHMS
    BOOTH, KS
    LUEKER, GS
    [J]. JOURNAL OF COMPUTER AND SYSTEM SCIENCES, 1976, 13 (03) : 335 - 379
  • [8] On the tandem duplication-random loss model of genome rearrangement
    Chaudhuri, Kamalika
    Chen, Kevin
    Mihaescu, Radu
    Rao, Satish
    [J]. PROCEEDINGS OF THE SEVENTHEENTH ANNUAL ACM-SIAM SYMPOSIUM ON DISCRETE ALGORITHMS, 2006, : 564 - +
  • [9] Evolution of the deep-sea gulper eel mitochondrial genomes: Large-scale gene rearrangements originated within the eels
    Inoue, JG
    Miya, M
    Tsukamoto, K
    Nishida, M
    [J]. MOLECULAR BIOLOGY AND EVOLUTION, 2003, 20 (11) : 1917 - 1924
  • [10] Moret BME, 2005, MATHEMATICS OF EVOLUTION AND PHYLOGENY, P321
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