Common Interval Rearrangement EXplorer

heuristically exploring mitochondrial rearrangements based on common intervals

start

start here and input data.

overview

CREx is a tool for comparisons of gene order data. it uses a data structure called strong common interval tree (Bérard et al. 2007) - also called pq-tree (Booth an Lueker 1976). it heuristically determines rearrangement scenarios to transform one gene order into the other. the main features of CREx are:

with the help of a distance matrix the used can identify similar gene orders, which can be selected for pairwise comparisions.
with the help of the interval tree the user can identify regions of similarity between two gene orders
the heuristic method to determine genome rearrangement scenarios between two given gene orders includes transpositions, reverse transpositions, reversals, and tandem-duplication-random-loss (tdrl) events
a highlight is the identification of tandem duplication random loss rearrangements (Chaudhuri et al. 2006) which are usually quite difficult to identify manually. these operations can be of special interest because they can provide information on the evolutionary direction, in contrast to the other rearrangements.

please cite:
Matthias Bernt, Daniel Merkle, Kai Ramsch, Guido Fritzsch, Marleen Perseke, Detlef Bernhard, Martin Schlegel, Peter Stadler, and Martin Middendorf
CREx: Inferring Genomic Rearrangements Based on Common Intervals
Bioinformatics, 2007, 23(21):2957-2958 pdf link

documentation and examples

a short tutorial for the usage of CREx is presented here. the technical details of CREx and a short tutorial for the interpretation of the results are documented here. we have compiled a set of examples which demonstrates the capabilities of CREx.

contact

authors:	matthias bernt, daniel merkle, martin middendorf
	( parallel computing and complex systems group , university of leipzig ).
contact:	bernt (at) informatik (dot) uni-leipzig (dot) de

obtaining input data for CREx

for generating a consistent set of gene orders you might use use our software for the automatic annotation of mitochondrial genomes MITOS.

gene order data for the comparison can also be obtained from MitoZoa

usage of CRex

A. Golombek, S. Tobergte, M. P. Nesnidal, G. Purschke, T. H. Struck
Mitochondrial genomes to the rescue - Diurodrilidae in the myzostomid trap
Molecular Phylogenetics and Evolution 2013 link

M. Perseke, A. Golombek, M. Schlegel, T. H. Struck
The impact of mitochondrial genome analyses on the understanding of deuterostome phylogeny
Molecular Phylogenetics and Evolution 2013, 66(3):898-905 link

Feng-Jiau Lin, Yuan Liu, Zhongli Sha, Ling M Tsang, Ka H Chu, Tin-Yam Chan, Ruiyu Liu and Zhaoxia Cui
Evolution and phylogeny of the mud shrimps (Crustacea: Decapoda) revealed from complete mitochondrial genomes
BMC Genomics 2012, 13:631 link

Chen HX, Sun SC, Sundberg P, Ren WC, Norenburg JL
A comparative study of nemertean complete mitochondrial genomes, including two new ones for Nectonemertes cf. mirabilis and Zygeupolia rubens, may elucidate the fundamental pattern for the phylum Nemertea.
BMC Genomics. 2012 13:139 link

L Krebes and R Bastrop
The mitogenome of Gammarus duebeni (Crustacea Amphipoda): A new gene order and non-neutral sequence evolution of tandem repeats in the control region
Comparative Biochemistry and Physiology Part D: Genomics and Proteomics link

A Duò, R Bruggmann, S Zoller, M Bernt, CR Grünig
Mitochondrial genome evolution in species belonging to the Phialocephala fortinii sl-Acephala applanata species complex
BMC genomics 2012 13(1), 166 link

BL Webster and DTJ Littlewood
Mitochondrial gene order change in Schistosoma (Platyhelminthes: Digenea: Schistosomatidae)
International Journal for Parasitology 2012 42(3):313-321 link

M P Nesnidal, M Helmkampf, I Bruchhaus and B Hausdorf
The complete mitochondrial genome of Flustra foliacea (Ectoprocta, Cheilostomata) - compositional bias affects phylogenetic analyses of lophotrochozoan relationships
BMC Genomics 2011, 12:572 link

M Wang, S Sun, C Li and X Shen
Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies
BMC Genomics 2011, 12:73 link

M Perseke, J Hetmank, M Bernt, P F Stadler, M Schlegel and D Bernhard
The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia) reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria
BMC Evolutionary Biology 2011, 11:134 link

A Mwinyi, X Bailly, S J Bourlat, U Jondelius, D Timothy J Littlewood and L Podsiadlowski
The phylogenetic position of Acoela as revealed by the complete mitochondrial genome of Symsagittifera roscoffensis
BMC Evolutionary Biology 2010, 10:309 link

T Stach, A Braband and L Podsiadlowski
Erosion of phylogenetic signal in tunicate mitochondrial genomes on different levels of analysis
Molecular Phylogenetics and Evolution 55(3):860-870, 2010 link

M Perseke, D Bernhard, G Fritzsch, F Brümmer, P F. Stadler and M Schlegel
Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: Insights in phylogenetic relationships of Echinodermata
Molecular Phylogenetics and Evolution 56(1):201-211, 2010 link

W Dermauw, T Van Leeuwen, B Vanholme and L Tirry
The complete mitochondrial genome of the house dust mite Dermatophagoides pteronyssinus (Trouessart): a novel gene arrangement among arthropods
BMC Genomics 2009, 10:107 link

C Bleidorn, N Hill, C Erséus and R Tiedemann
On the role of character loss in orbiniid phylogeny (Annelida): Molecules vs. morphology
Molecular Phylogenetics and Evolution 2009, 52(1):57-69 link

M M Bauzà-Ribot, D Jaume, C Juan and J Pons
The complete mitochondrial genome of the subterranean crustacean Metacrangonyx longipes (Amphipoda): A unique gene order and extremely short control region
Mitochondrial DNA 2009 20(4):88-99 link