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» A computational genomics pipeline for prokaryotic sequencing...
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BMCBI
2008
104views more  BMCBI 2008»
13 years 6 months ago
ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS)
Background: Genome survey sequences (GSS) offer a preliminary global view of a genome since, unlike ESTs, they cover coding as well as non-coding DNA and include repetitive region...
Thomas D. Otto, Leonardo H. F. Gomes, Marcelo Alve...
BMCBI
2005
127views more  BMCBI 2005»
13 years 5 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
NAR
2007
109views more  NAR 2007»
13 years 5 months ago
GeneTrees: a phylogenomics resource for prokaryotes
The GeneTrees phylogenomics system pursues comparative genomic analyses from the perspective of gene phylogenies for individual genes. The GeneTrees project has the goal of provid...
Yuying Tian, Allan W. Dickerman
BMCBI
2007
154views more  BMCBI 2007»
13 years 6 months ago
Bounds on the distribution of the number of gaps when circles and lines are covered by fragments: Theory and practical applicati
Background: The question of how a circle or line segment becomes covered when random arcs are marked off has arisen repeatedly in bioinformatics. The number of uncovered gaps is o...
John Moriarty, Julian R. Marchesi, Anthony Metcalf...
BMCBI
2011
13 years 14 days ago
Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies
Background: Next-generation sequencing technologies allow genomes to be sequenced more quickly and less expensively than ever before. However, as sequencing technology has improve...
Joshua Wetzel, Carl Kingsford, Mihai Pop