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
submitted.
pdf
see also:
Marleen Perseke, Guido Fritzsch, Kai Ramsch, Matthias Bernt, Daniel Merkle, Martin Middendorf, Detlef Bernhard, Peter Stadler, Martin Schlegel
Evolution of Mitochondrial Gene Orders in Echinoderms
submitted.
pdf
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
final notes
- bugs: none known
- do not hesitate to write us an email if you have questions