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» Sequence Database Search Using Jumping Alignments
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BMCBI
2004
102views more  BMCBI 2004»
15 years 3 months ago
FRAGS: estimation of coding sequence substitution rates from fragmentary data
Background: Rates of substitution in protein-coding sequences can provide important insights into evolutionary processes that are of biomedical and theoretical interest. Increased...
Estienne C. Swart, Winston A. Hide, Cathal Seoighe
BMCBI
2005
94views more  BMCBI 2005»
15 years 3 months ago
Measuring similarities between transcription factor binding sites
Background: Collections of transcription factor binding profiles (Transfac, Jaspar) are essential to identify regulatory elements in DNA sequences. Subsets of highly similar profi...
Szymon M. Kielbasa, Didier Gonze, Hanspeter Herzel
PETRA
2009
ACM
15 years 9 months ago
Towards faster activity search using embedding-based subsequence matching
Event search is the problem of identifying events or activity of interest in a large database storing long sequences of activity. In this paper, our topic is the problem of identi...
Panagiotis Papapetrou, Paul Doliotis, Vassilis Ath...
BMCBI
2007
135views more  BMCBI 2007»
15 years 3 months ago
RECOVIR: An application package to automatically identify some single stranded RNA viruses using capsid protein residues that un
Background: Most single stranded RNA (ssRNA) viruses mutate rapidly to generate large number of strains having highly divergent capsid sequences. Accurate strain recognition in un...
Dianhui Zhu, George E. Fox, Sugoto Chakravarty
ENGL
2008
78views more  ENGL 2008»
15 years 3 months ago
Threshold for Positional Weight Matrix
In biological sequence research, the positional weight matrix (PWM) is often used to search for putative transcription factor binding sites. A set of experimentally verified oligon...
Yunlian Pan, Sieu Phan