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Algorithms for Genome Rearrangement by Double Cut and Join
Published on Oct 02, 20124490 Views
Genome evolution on the basis of gene order has been modeled by a variety of rearrangement operations such as inversions, translocations, transpositions, block interchanges, fusions and fissions. Th
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Algorithms for Genome Rearrangement by Double Cut and Join00:00
Outline00:20
Genome evolution (1)00:26
Genome evolution (2)00:47
Motivation03:41
What happens in detail? (1)05:53
What happens in detail? (2)11:54
Questions to be asked13:58
Some history (2 genomes) (1)15:54
Some history (2 genomes) (2)16:56
Towards formal modeling17:10
Double Cut and Join (DCJ)19:22
Graphs with vertices of degree one or two19:46
The formal problem (1)21:47
The formal problem (2)24:08
DCJ distance and sorting24:49
Adjacency graph26:46
Transforming A into B28:27
Algorithm32:22
The DCJ distance33:06
The solution space of sorting by DCJ36:50
Relation to other models39:40
Relationship of distances41:45
General HP distance problem (1)43:31
General HP distance problem (2)45:04
Restricted DCJ48:33
Software: UNIMoG50:31
Further applications of the DCJ model50:50
Insertions, deletions, substitutions51:07
Insertion/Deletion52:12
The DCJ-indel model (1)52:40
The DCJ-indel model (2)53:39
On the weight of indels56:01
A posteriori correction57:42
More plausible distances?59:01
DCJ with substitutions59:47
Summary and Conclusion59:50
Acknowledgments01:01:39
Thank you!01:02:16
References01:02:29