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» Approximate Similarity Search in Genomic Sequence Databases ...
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NAR
2008
122views more  NAR 2008»
13 years 4 months ago
The Rice Annotation Project Database (RAP-DB): 2008 update
The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated ann...
NAR
2011
253views Computer Vision» more  NAR 2011»
12 years 7 months ago
tRNADB-CE 2011: tRNA gene database curated manually by experts
We updated the tRNADB-CE by analyzing 939 complete and 1301 draft genomes of prokaryotes and eukaryotes, 171 complete virus genomes, 121 complete chloroplast genomes and approxima...
Takashi Abe, Toshimichi Ikemura, Junichi Sugahara,...
BMCBI
2008
130views more  BMCBI 2008»
13 years 4 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
123views more  BMCBI 2008»
13 years 4 months ago
Shape based indexing for faster search of RNA family databases
Background: Most non-coding RNA families exert their function by means of a conserved, common secondary structure. The Rfam data base contains more than five hundred structurally ...
Stefan Janssen, Jens Reeder, Robert Giegerich
BMCBI
2005
131views more  BMCBI 2005»
13 years 4 months ago
Functional annotation by identification of local surface similarities: a novel tool for structural genomics
Background: Protein function is often dependent on subsets of solvent-exposed residues that may exist in a similar three-dimensional configuration in non homologous proteins thus ...
Fabrizio Ferrè, Gabriele Ausiello, Andreas ...