Modeling sequence evolution under domain constraints Long Description (required)
REvolver is a program to simulate protein sequence evolution. REvolver automatically integrates domain information described by a profile Hidden Markov Model (pHMM) into the simulation. In the simulation of protein evolution it often had been assumed that sites evolve identically and independently from each other. This simplification is necessary since information concerning site specific evolution is frequently unavailable. However, homologous sequences and domains have been collected, aligned, and pHMMs built. The pHMM describes the variability and shared characteristics of sequences that share a common ancestor. Here we do have knowledge about what sites are conserved, at what positions in the sequences insertions are more likely, or what sites can be deleted. Pfam (Finn et al., 2010) and SMART (Letunic, Doerks and Bork, 2009) are examples for databases providing such data. REvolver is the first method, for simulating protein sequence evolution that integrates this pre-existing information about evolution in an automatic fashion. http://www.cibiv.at/software/revolver/
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Summary of Proposed Changes Current Citations/Applications
[Pubmed ID: 22383532 ],
Koestler T, von Haeseler A, Ebersberger I ,
REvolver: modeling sequence evolution under domain constraints. ,
Mol Biol Evol ,
09-01-2012 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=22383532, Primary Citation