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BMCBI
2005
127views more  BMCBI 2005»
10 years 11 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
BMCBI
2005
133views more  BMCBI 2005»
10 years 11 months ago
Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops
Background: Public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. The available data offers new opportunities to add...
Hélène Chiapello, I. Bourgait, F. So...
TCS
2008
10 years 11 months ago
A small trip in the untranquil world of genomes: A survey on the detection and analysis of genome rearrangement breakpoints
Genomes are dynamic molecules that are constantly undergoing mutations and rearrangements. The latter are large scale changes in a genome organisation that participate in the evol...
Claire Lemaitre, Marie-France Sagot
IJDMB
2007
110views more  IJDMB 2007»
10 years 11 months ago
Transductive learning with EM algorithm to classify proteins based on phylogenetic profiles
: Phylogenetic profiles of proteins  strings of ones and zeros encoding respectively the presence and absence of proteins in a group of genomes  have recently been used to id...
Roger A. Craig, Li Liao
NAR
2006
81views more  NAR 2006»
10 years 11 months ago
Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser
The Yeast Gene Order Browser (YGOB) is an online tool designed to facilitate the comparative genomic visualization and appraisal of synteny within and between the genomes of seven...
Kevin P. Byrne, Kenneth H. Wolfe
NAR
2006
170views more  NAR 2006»
10 years 11 months ago
The UCSC Genome Browser Database: update 2006
The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major m...
Angela S. Hinrichs, Donna Karolchik, Robert Baerts...
NAR
2006
119views more  NAR 2006»
10 years 11 months ago
ChloroplastDB: the Chloroplast Genome Database
The Chloroplast Genome Database (ChloroplastDB) is an interactive, web-based database for fully sequenced plastid genomes, containing genomic, protein, DNA and RNA sequences, gene...
Liying Cui, Narayanan Veeraraghavan, Alexander Ric...
JEA
2008
97views more  JEA 2008»
10 years 12 months ago
Approximating the true evolutionary distance between two genomes
As more and more genomes are sequenced, evolutionary biologists are becoming increasingly interested in evolution at the level of whole genomes, in scenarios in which the genome e...
Krister M. Swenson, Mark Marron, Joel V. Earnest-D...
JCO
2008
76views more  JCO 2008»
10 years 12 months ago
On the inapproximability of the exemplar conserved interval distance problem of genomes
In this paper we present two main results about the inapproximability of the exemplar conserved interval distance problem of genomes. First, we prove that it is NP-complete to deci...
Zhixiang Chen, Richard H. Fowler, Bin Fu, Binhai Z...
JCB
2008
144views more  JCB 2008»
10 years 12 months ago
Multi-Break Rearrangements and Breakpoint Re-Uses: From Circular to Linear Genomes
Multi-break rearrangements break a genome into multiple fragments and further glue them together in a new order. While 2-break rearrangements represent standard reversals, fusions...
Max A. Alekseyev
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