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FCCM
2007
IEEE
134views VLSI» more  FCCM 2007»
15 years 6 months ago
FPGA-accelerated seed generation in Mercury BLASTP
BLASTP is the most popular tool to perform comparative sequence analysis of protein sequences. An exponential increase in the size of protein sequence databases in recent years, h...
Arpith C. Jacob, Joseph M. Lancaster, Jeremy Buhle...
ALMOB
2006
89views more  ALMOB 2006»
14 years 12 months ago
On the maximal cliques in c-max-tolerance graphs and their application in clustering molecular sequences
Given a set S of n locally aligned sequences, it is a needed prerequisite to partition it into groups of very similar sequences to facilitate subsequent computations, such as the ...
Katharina Anna Lehmann, Michael Kaufmann, Stephan ...
BMCBI
2006
129views more  BMCBI 2006»
14 years 12 months ago
Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps
Background: Protein sequence alignment is one of the basic tools in bioinformatics. Correct alignments are required for a range of tasks including the derivation of phylogenetic t...
Tomas Ohlson, Varun Aggarwal, Arne Elofsson, Rober...
BMCBI
2008
200views more  BMCBI 2008»
14 years 12 months ago
Defining functional distances over Gene Ontology
Background: A fundamental problem when trying to define the functional relationships between proteins is the difficulty in quantifying functional similarities, even when well-stru...
Angela del Pozo, Florencio Pazos, Alfonso Valencia
BIOCOMP
2008
15 years 1 months ago
Prediction of Protein Function Using Graph Container and Message Passing
We introduce a novel parameter called container flux, which is used to measure the information sharing capacity between two distinct nodes in a graph. Other useful information, bot...
Hongbo Zhou, Qiang Shawn Cheng, Mehdi Zargham