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» Patterns for Refinement Automation
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BMCBI
2007
82views more  BMCBI 2007»
13 years 6 months ago
Visualization of three-way comparisons of omics data
Background: Density plot visualizations (also referred to as heat maps or color maps) are widely used in different fields including large-scale omics studies in biological science...
Richard Baran, Martin Robert, Makoto Suematsu, Tom...
BMCBI
2008
130views more  BMCBI 2008»
13 years 6 months ago
A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm
Background: The process of horizontal gene transfer (HGT) is believed to be widespread in Bacteria and Archaea, but little comparative data is available addressing its occurrence ...
Sheila Podell, Terry Gaasterland, Eric E. Allen
BMCBI
2006
120views more  BMCBI 2006»
13 years 6 months ago
Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding prote
Background: When accurate models for the divergent evolution of protein sequences are integrated with complementary biological information, such as folded protein structures, anal...
Michael E. Bradley, Steven A. Benner
BMCBI
2006
112views more  BMCBI 2006»
13 years 6 months ago
A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database
Background: We present here the PhIGs database, a phylogenomic resource for sequenced genomes. Although many methods exist for clustering gene families, very few attempt to create...
Paramvir S. Dehal, Jeffrey L. Boore
BMCBI
2006
135views more  BMCBI 2006»
13 years 6 months ago
TF Target Mapper: A BLAST search tool for the identification of Transcription Factor target genes
Background: In the current era of high throughput genomics a major challenge is the genome-wide identification of target genes for specific transcription factors. Chromatin immuno...
Sebastiaan Horsman, Michael J. Moorhouse, Victor C...