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BMCBI
2008
130views more  BMCBI 2008»
14 years 11 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
2008
99views more  BMCBI 2008»
14 years 11 months ago
Multiple organism algorithm for finding ultraconserved elements
Background: Ultraconserved elements are nucleotide or protein sequences with 100% identity (no mismatches, insertions, or deletions) in the same organism or between two or more or...
Scott Christley, Neil F. Lobo, Gregory R. Madey
BMCBI
2011
14 years 6 months ago
N-gram analysis of 970 microbial organisms reveals presence of biological language models
Background: It has been suggested previously that genome and proteome sequences show characteristics typical of natural-language texts such as “signature-style” word usage ind...
Hatice U. Osmanbeyoglu, Madhavi Ganapathiraju
CDB
2004
Springer
172views Database» more  CDB 2004»
15 years 5 months ago
Constraint Database Solutions to the Genome Map Assembly Problem
Abstract. Long DNA sequences have to be cut using restriction enzymes into small fragments whose lengths and/or nucleotide sequences can be analyzed by currently available technolo...
Viswanathan Ramanathan, Peter Z. Revesz
RECOMB
2008
Springer
16 years 21 hour ago
Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer
Abstract. One phylogeny-based approach to horizontal gene transfer (HGT) detection entails comparing the topology of a gene tree to that of the species tree, and using their differ...
Cuong Than, Guohua Jin, Luay Nakhleh