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» The Distance Between Randomly Constructed Genomes
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BMCBI
2010
135views more  BMCBI 2010»
13 years 6 months ago
GIGA: a simple, efficient algorithm for gene tree inference in the genomic age
Background: Phylogenetic relationships between genes are not only of theoretical interest: they enable us to learn about human genes through the experimental work on their relativ...
Paul D. Thomas
BMCBI
2005
127views more  BMCBI 2005»
13 years 6 months ago
Genomes are covered with ubiquitous 11 bp periodic patterns, the "class A flexible patterns"
Background: The genomes of prokaryotes and lower eukaryotes display a very strong 11 bp periodic bias in the distribution of their nucleotides. This bias is present throughout a g...
Etienne Larsabal, Antoine Danchin
IPL
2006
104views more  IPL 2006»
13 years 6 months ago
The communication complexity of the Hamming distance problem
We investigate the randomized and quantum communication complexity of the HAMMING DISTANCE problem, which is to determine if the Hamming distance between two n-bit strings is no l...
Wei Huang, Yaoyun Shi, Shengyu Zhang, Yufan Zhu
PSB
2003
13 years 7 months ago
MAP: Searching Large Genome Databases
A number of biological applications require comparison of large genome strings. Current techniques suffer from both disk I/O and computational cost because of extensive memory req...
Tamer Kahveci, Ambuj K. Singh
JCB
2006
124views more  JCB 2006»
13 years 6 months ago
The Average Common Substring Approach to Phylogenomic Reconstruction
We describe a novel method for efficient reconstruction of phylogenetic trees, based on sequences of whole genomes or proteomes, whose lengths may greatly vary. The core of our me...
Igor Ulitsky, David Burstein, Tamir Tuller, Benny ...