Sybil: Methods and Software for Multiple Genome Comparison and Visualization

2007 ◽  
pp. 93-108 ◽  
Author(s):  
Jonathan Crabtree ◽  
Samuel V. Angiuoli ◽  
Jennifer R. Wortman ◽  
Owen R. White
Keyword(s):  
Genome Comparison ◽  
Multiple Genome

scholarly journals TWO PLUS TWO DOES NOT EQUAL THREE: STATISTICAL TESTS FOR MULTIPLE GENOME COMPARISON

2008 ◽  
Vol 06 (01) ◽  
pp. 1-22 ◽  
Author(s):  
NARAYANAN RAGHUPATHY ◽  
ROSE HOBERMAN ◽  
DANNIE DURAND
Keyword(s):  
Comparative Genomics ◽  
Large Scale ◽  
Statistical Tests ◽  
Gene Clusters ◽  
Genome Comparison ◽  
Pairwise Comparisons ◽  
Multiple Genome ◽  
Number Of Genes ◽  
Multiple Species ◽  
Combine Evidence

Gene clusters that span three or more chromosomal regions are of increasing importance, yet statistical tests to validate such clusters are in their infancy. Current approaches either conduct several pairwise comparisons or consider only the number of genes that occur in all of the regions. In this paper, we provide statistical tests for clusters spanning exactly three regions based on genome models of typical comparative genomics problems, including analysis of conserved linkage within multiple species and identification of large-scale duplications. Our tests are the first to combine evidence from genes shared among all three regions and genes shared between pairs of regions. We show that our tests of clusters spanning three regions are more sensitive than existing approaches, and can thus be used to identify more diverged homologous regions.

scholarly journals An alternative approach to multiple genome comparison

2011 ◽  
Vol 39 (15) ◽  
pp. e101-e101 ◽  
Author(s):  
Alban Mancheron ◽  
Raluca Uricaru ◽  
Eric Rivals
Keyword(s):  
Genome Comparison ◽  
Multiple Genome ◽  
Alternative Approach

scholarly journals Chaining algorithms for multiple genome comparison

2005 ◽  
Vol 3 (2-4) ◽  
pp. 321-341 ◽  
Author(s):  
Mohamed Ibrahim Abouelhoda ◽  
Enno Ohlebusch
Keyword(s):  
Genome Comparison ◽  
Multiple Genome

scholarly journals Multiple-Genome Comparison Reveals New Loci for Mycobacterium Species Identification

2010 ◽  
Vol 49 (1) ◽  
pp. 144-153 ◽  
Author(s):  
J. Dai ◽  
Y. Chen ◽  
S. Dean ◽  
J. G. Morris ◽  
M. Salfinger ◽  
...  
Keyword(s):  
Species Identification ◽  
Genome Comparison ◽  
Mycobacterium Species ◽  
Multiple Genome

STEINER POINTS IN THE SPACE OF GENOME REARRANGEMENTS

1996 ◽  
Vol 07 (01) ◽  
pp. 1-9 ◽  
Author(s):  
DAVID SANKOFF ◽  
GOPALAKRISHNAN SUNDARAM ◽  
JOHN KECECIOGLU
Keyword(s):  
Local Search ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Sequence Comparison ◽  
Genome Rearrangements ◽  
Genome Comparison ◽  
Distance Metrics ◽  
Multiple Sequence ◽  
Multiple Genome ◽  
Steiner Points

We present some experiences with the problem of multiple genome comparison, analogous to multiple sequence alignment in sequence comparison, under the inversion and transposition distance metrics, given a fixed phylogeny. We first describe a heuristic for the case in which phylogeny is a star on three vertices and then use this to approximate the multiple genome comparison problem via local search.

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