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BMCBI
2010
121views more  BMCBI 2010»
10 years 12 months ago
Reconstructing genome trees of prokaryotes using overlapping genes
Background: Overlapping genes (OGs) are defined as adjacent genes whose coding sequences overlap partially or entirely. In fact, they are ubiquitous in microbial genomes and more ...
Chih-Hsien Cheng, Chung-Han Yang, Hsien-Tai Chiu, ...
BIOCOMP
2007
11 years 1 months ago
Towards Phylogenomic Reconstruction
Reconstructing phylogenies is one of the primary objectives in evolution studies. Efficient software to reconstruct phylogenies based on isolated genes has existed for decades, ye...
Le Vinh, Andres Varon, Daniel Janies, Ward Wheeler
AAAI
2010
11 years 1 months ago
Genome Rearrangement: A Planning Approach
Evolutionary trees of species can be reconstructed by pairwise comparison of their entire genomes. Such a comparison can be quantified by determining the number of events that cha...
Tansel Uras, Esra Erdem
STOC
1995
ACM
194views Algorithms» more  STOC 1995»
11 years 3 months ago
Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
Genomes frequently evolve by reversals ␳(i, j) that transform a gene order ␲1 . . . ␲i␲iϩ1 . . . ␲jϪ1␲j . . . ␲n into ␲1 . . . ␲i␲jϪ1 . . . ␲iϩ1␲j . . ....
Sridhar Hannenhalli, Pavel A. Pevzner
CSB
2004
IEEE
113views Bioinformatics» more  CSB 2004»
11 years 3 months ago
Shannon Information in Complete Genomes
Shannon information in the genomes of all completely sequenced prokaryotes and eukaryotes are measured in word lengths of two to ten letters. It is found that in a scale-dependent...
Chang-Heng Chang, Li-Ching Hsieh, Ta-Yuan Chen, Ho...
BIBE
2004
IEEE
11 years 3 months ago
Phylogenetic Reconstruction from Arbitrary Gene-Order Data
Phylogenetic reconstruction from gene-order data has attracted attention from both biologists and computer scientists over the last few years. So far, our software suite GRAPPA is...
Jijun Tang, Bernard M. E. Moret, Liying Cui, Claud...
RECOMB
1997
Springer
11 years 4 months ago
On the complexity and approximation of syntenic distance
The paper studies the computational complexity and approximation algorithms for a new evolutionary distance between multi-chromosomal genomes introduced recently by Ferretti, Nade...
Bhaskar DasGupta, Tao Jiang, Sampath Kannan, Ming ...
IPPS
2002
IEEE
11 years 4 months ago
Aligning Two Fragmented Sequences
Upon completion of the human and mouse genome sequences, world-wide sequencing capacity will turn to other complex organisms. Current strategies call for many of these genomes to ...
Vamsi Veeramachaneni, Piotr Berman, Webb Miller
WABI
2004
Springer
100views Bioinformatics» more  WABI 2004»
11 years 5 months ago
Reversing Gene Erosion - Reconstructing Ancestral Bacterial Genomes from Gene-Content and Order Data
In the last few years, it has become routine to use gene-order data to reconstruct phylogenies, both in terms of edge distances (parsimonious sequences of operations that transform...
Joel V. Earnest-DeYoung, Emmanuelle Lerat, Bernard...
CPM
2004
Springer
108views Combinatorics» more  CPM 2004»
11 years 5 months ago
Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences
A popular approach in comparative genomics is to locate groups or clusters of orthologous genes in multiple genomes and to postulate functional association between the genes contai...
Thomas Schmidt, Jens Stoye
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