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» ANNALIST - ANNotation ALIgnment and Scoring Tool
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RECOMB
2009
Springer
14 years 6 months ago
Learning Models for Aligning Protein Sequences with Predicted Secondary Structure
Accurately aligning distant protein sequences is notoriously difficult. A recent approach to improving alignment accuracy is to use additional information such as predicted seconda...
Eagu Kim, Travis J. Wheeler, John D. Kececioglu
BMCBI
2010
137views more  BMCBI 2010»
13 years 5 months ago
Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments
Background: While the pairwise alignments produced by sequence similarity searches are a powerful tool for identifying homologous proteins - proteins that share a common ancestor ...
Michael L. Sierk, Michael E. Smoot, Ellen J. Bass,...
JCB
2000
101views more  JCB 2000»
13 years 5 months ago
Evaluation Measures of Multiple Sequence Alignments
Multiple sequence alignments (MSAs) are frequently used in the study of families of protein sequences or DNA/RNA sequences. They are a fundamental tool for the understanding of th...
Gaston H. Gonnet, Chantal Korostensky, Steven A. B...
BMCBI
2005
138views more  BMCBI 2005»
13 years 5 months ago
Detailed protein sequence alignment based on Spectral Similarity Score (SSS)
Background: The chemical property and biological function of a protein is a direct consequence of its primary structure. Several algorithms have been developed which determine ali...
Kshitiz Gupta, Dina Thomas, S. V. Vidya, K. V. Ven...
BMCBI
2008
123views more  BMCBI 2008»
13 years 5 months ago
A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences
Background: The structure of many eukaryotic cell regulatory proteins is highly modular. They are assembled from globular domains, segments of natively disordered polypeptides and...
Claudia Chica, Alberto Labarga, Cathryn M. Gould, ...