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» A Flexible Algorithm for Pairwise Protein Structure Alignmen...
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134
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NAR
2007
152views more  NAR 2007»
15 years 3 months ago
COMPASS server for remote homology inference
COMPASS is a method for homology detection and local alignment construction based on the comparison of multiple sequence alignments (MSAs). The method derives numerical profiles f...
Ruslan Sadreyev, Ming Tang, Bong-Hyun Kim, Nick V....
146
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BMCBI
2010
104views more  BMCBI 2010»
15 years 3 months ago
Parameters for accurate genome alignment
Background: Genome sequence alignments form the basis of much research. Genome alignment depends on various mundane but critical choices, such as how to mask repeats and which sco...
Martin C. Frith, Michiaki Hamada, Paul Horton
136
Voted
BMCBI
2006
117views more  BMCBI 2006»
15 years 3 months ago
Incorporating background frequency improves entropy-based residue conservation measures
Background: Several entropy-based methods have been developed for scoring sequence conservation in protein multiple sequence alignments. High scoring amino acid positions may corr...
Kai Wang, Ram Samudrala
237
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CSB
2004
IEEE
208views Bioinformatics» more  CSB 2004»
15 years 7 months ago
Pair Stochastic Tree Adjoining Grammars for Aligning and Predicting Pseudoknot RNA Structures
Motivation: Since the whole genome sequences for many species are currently available, computational predictions of RNA secondary structures and computational identifications of t...
Hiroshi Matsui, Kengo Sato, Yasubumi Sakakibara
108
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JCC
2007
131views more  JCC 2007»
15 years 3 months ago
An extended dead-end elimination algorithm to determine gap-free lists of low energy states
: Proteins are flexible systems and commonly populate several functionally important states. To understand protein function, these states and their energies have to be identified...
Edda Kloppmann, G. Matthias Ullmann, Torsten Becke...