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» Database Searching with DNA and Protein Sequences: An Introd...
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BMCBI
2002
120views more  BMCBI 2002»
13 years 7 months ago
tacg - a grep for DNA
Background: Pattern matching is the core of bioinformatics; it is used in database searching, restriction enzyme mapping, and finding open reading frames. It is done repeatedly ov...
Harry Mangalam
NAR
2007
90views more  NAR 2007»
13 years 7 months ago
The SUPERFAMILY database in 2007: families and functions
The SUPERFAMILY database provides protein domain assignments, at the SCOP ‘superfamily’ level, for the predicted protein sequences in over 400 completed genomes. A superfamily...
Derek Wilson, Martin Madera, Christine Vogel, Cyru...
ISB
2002
140views more  ISB 2002»
13 years 7 months ago
Computer system "Gene Discovery" for promoter structure analysis
Data Mining and Knowledge Discovery techniques proved to be efficient tools for variety of complex tasks in biology including DNA research. This paper presents implementation of th...
Eugenii E. Vityaev, Yuri L. Orlov, Oleg V. Vishnev...
IPPS
2007
IEEE
14 years 1 months ago
High Performance Database Searching with HMMer on FPGAs
1 Profile Hidden Markov Models (profile HMMs) are used as a popular bioinformatics tool for sensitive database searching, e.g. a set of not annotated protein sequences is compared...
Timothy F. Oliver, Leow Yuan Yeow, Bertil Schmidt
BMCBI
2002
133views more  BMCBI 2002»
13 years 7 months ago
Identification and characterization of subfamily-specific signatures in a large protein superfamily by a hidden Markov model app
Background: Most profile and motif databases strive to classify protein sequences into a broad spectrum of protein families. The next step of such database studies should include ...
Kevin Truong, Mitsuhiko Ikura