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» Discriminative Locality Alignment
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149
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BIBE
2008
IEEE
142views Bioinformatics» more  BIBE 2008»
15 years 9 months ago
Optimizing performance, cost, and sensitivity in pairwise sequence search on a cluster of PlayStations
— The Smith-Waterman algorithm is a dynamic programming method for determining optimal local alignments between nucleotide or protein sequences. However, it suffers from quadrati...
Ashwin M. Aji, Wu-chun Feng
115
Voted
BMCBI
2008
145views more  BMCBI 2008»
15 years 2 months ago
The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction
Background: Amino acids responsible for structure, core function or specificity may be inferred from multiple protein sequence alignments where a limited set of residue types are ...
Jonathan R. Manning, Emily R. Jefferson, Geoffrey ...
129
Voted
BMCBI
2002
101views more  BMCBI 2002»
15 years 2 months ago
Total sequence decomposition distinguishes functional modules, "molegos" in apurinic/apyrimidinic endonucleases
Background: Total sequence decomposition, using the web-based MASIA tool, identifies areas of conservation in aligned protein sequences. By structurally annotating these motifs, t...
Catherine H. Schein, Numan Özgün, Tadahi...
133
Voted
NAR
2007
130views more  NAR 2007»
15 years 2 months ago
The SLiMDisc server: short, linear motif discovery in proteins
Short, linear motifs (SLiMs) play a critical role in many biological processes, particularly in protein–protein interactions. Overrepresentation of convergent occurrences of mot...
Norman E. Davey, Richard J. Edwards, Denis C. Shie...
159
Voted
BMCBI
2011
14 years 6 months ago
Conotoxin Protein Classification Using Free Scores of Words and Support Vector Machines
Background: Conotoxin has been proven to be effective in drug design and could be used to treat various disorders such as schizophrenia, neuromuscular disorders and chronic pain. ...
Nazar Zaki, Stefan Wolfsheimer, Grégory Nue...