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BMCBI
2005
106views more  BMCBI 2005»
13 years 5 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...
BMCBI
2010
138views more  BMCBI 2010»
13 years 5 months ago
Sigma-2: Multiple sequence alignment of non-coding DNA via an evolutionary model
Background: While most multiple sequence alignment programs expect that all or most of their input is known to be homologous, and penalise insertions and deletions, this is not a ...
Gayathri Jayaraman, Rahul Siddharthan
BMCBI
2005
97views more  BMCBI 2005»
13 years 5 months ago
Evolutionary distance estimation and fidelity of pair wise sequence alignment
Background: Evolutionary distances are a critical measure in comparative genomics and molecular evolutionary biology. A simulation study was used to examine the effect of alignmen...
Michael S. Rosenberg
PSB
2004
13 years 7 months ago
Phylogenetic Motif Detection by Expectation-Maximization on Evolutionary Mixtures
ct The preferential conservation of transcription factor binding sites implies that non-coding sequence data from related species will prove a powerful asset to motif discovery. We...
Alan M. Moses, Derek Y. Chiang, Michael B. Eisen
BMCBI
2008
144views more  BMCBI 2008»
13 years 5 months ago
Local conservation scores without a priori assumptions on neutral substitution rates
Background: Comparative genomics aims to detect signals of evolutionary conservation as an indicator of functional constraint. Surprisingly, results of the ENCODE project revealed...
Janis Dingel, Pavol Hanus, Niccolò Leonardi...