Multiple genome alignment based on longest path in directed acyclic graphs

2010 ◽  
Vol 6 (4) ◽  
pp. 366 ◽  
Author(s):  
Fangrui Ma ◽  
Jitender S. Deogun
Keyword(s):  
Directed Acyclic Graphs ◽  
Genome Alignment ◽  
Multiple Genome ◽  
Acyclic Graphs ◽  
Longest Path ◽  
Multiple Genome Alignment

A Nettree for Simple Paths with Length Constraint and the Longest Path in Directed Acyclic Graphs

2012 ◽  
Vol 35 (10) ◽  
pp. 2194 ◽  
Author(s):  
Yan LI ◽  
Le SUN ◽  
Huai-Zhong ZHU ◽  
You-Xi WU
Keyword(s):  
Directed Acyclic Graphs ◽  
Length Constraint ◽  
Acyclic Graphs ◽  
Longest Path ◽  
Simple Paths

scholarly journals progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

PLoS ONE ◽  
2010 ◽  
Vol 5 (6) ◽  
pp. e11147 ◽  
Author(s):  
Aaron E. Darling ◽  
Bob Mau ◽  
Nicole T. Perna
Keyword(s):  
Gene Gain ◽  
Genome Alignment ◽  
Multiple Genome ◽  
Gain Loss ◽  
Multiple Genome Alignment

scholarly journals Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era

2019 ◽  
Author(s):  
Joel Armstrong ◽  
Glenn Hickey ◽  
Mark Diekhans ◽  
Alden Deran ◽  
Qi Fang ◽  
...  
Keyword(s):  
Genome Alignment ◽  
Vertebrate Genome ◽  
Alignment Quality ◽  
Alignment Program ◽  
Progressive Alignment ◽  
Multiple Genome ◽  
Multiple Genome Alignment

AbstractCactus, a reference-free multiple genome alignment program, has been shown to be highly accurate, but the existing implementation scales poorly with increasing numbers of genomes, and struggles in regions of highly duplicated sequence. We describe progressive extensions to Cactus that enable reference-free alignment of tens to thousands of large vertebrate genomes while maintaining high alignment quality. We show that Cactus is capable of scaling to hundreds of genomes and beyond by describing results from an alignment of over 600 amniote genomes, which is to our knowledge the largest multiple vertebrate genome alignment yet created. Further, we show improvements in orthology resolution leading to downstream improvements in annotation.

Multiple Genome Alignment by Clustering Pairwise Matches

2005 ◽  
pp. 30-41 ◽  
Author(s):  
Jeong-Hyeon Choi ◽  
Kwangmin Choi ◽  
Hwan-Gue Cho ◽  
Sun Kim
Keyword(s):  
Genome Alignment ◽  
Multiple Genome ◽  
Multiple Genome Alignment

scholarly journals MafFilter: a highly flexible and extensible multiple genome alignment files processor

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 53 ◽  
Author(s):  
Julien Y Dutheil ◽  
Sylvain Gaillard ◽  
Eva H Stukenbrock
Keyword(s):  
Genome Alignment ◽  
Multiple Genome ◽  
Multiple Genome Alignment

scholarly journals Efficient multiple genome alignment

2002 ◽  
Vol 18 (Suppl 1) ◽  
pp. S312-S320 ◽  
Author(s):  
M. Hohl ◽  
S. Kurtz ◽  
E. Ohlebusch
Keyword(s):  
Genome Alignment ◽  
Multiple Genome ◽  
Multiple Genome Alignment
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