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» Stochastic Analysis of Amino Acid Substitution in Protein Sy...
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BMCBI
2005
106views more  BMCBI 2005»
13 years 7 months ago
SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution
Background: General protein evolution models help determine the baseline expectations for the evolution of sequences, and they have been extensively useful in sequence analysis an...
Andy Pang, Andrew D. Smith, Paulo A. S. Nuin, Elis...
CSB
2005
IEEE
136views Bioinformatics» more  CSB 2005»
14 years 29 days ago
Whole Genome Phylogeny Based on Clustered Signature String Composition
Peptide compositions constructed out of whole sets of protein sequences can be used as species signatures for phylogenetic analysis. To account for point mutations, an amino acid ...
Xiaomeng Wu, Guohui Lin, Xiu-Feng Wan, Dong Xu
NAR
2006
120views more  NAR 2006»
13 years 7 months ago
TreeDomViewer: a tool for the visualization of phylogeny and protein domain structure
Phylogenetic analysis and examination of protein domains allow accurate genome annotation and are invaluable to study proteins and protein complex evolution. However, two sequence...
Blaise T. F. Alako, Daphne Rainey, Harm Nijveen, J...
BMCBI
2010
104views more  BMCBI 2010»
13 years 7 months ago
A novel scoring function for discriminating hyperthermophilic and mesophilic proteins with application to predicting relative th
Background: The ability to design thermostable proteins is theoretically important and practically useful. Robust and accurate algorithms, however, remain elusive. One critical pr...
Yunqi Li, C. Russell Middaugh, Jianwen Fang
NAR
2008
107views more  NAR 2008»
13 years 7 months ago
MutDB: update on development of tools for the biochemical analysis of genetic variation
Understanding how genetic variation affects the molecular function of gene products is an emergent area of bioinformatic research. Here, we present updates to MutDB (http://www.mu...
Arti Singh, Adebayo Olowoyeye, Peter H. Baenziger,...