SAMEM v. 0.83 - Computer System for Analysis of Molecular Evolution Modes

The pipeline for genes analysis

Perform a remote search on protein sequences or protein-coding DNA sequences at NCBI GenBank using NetBlast. Perform a BLOSUM matrix construction.

Perform a procedures required for coding-sequence testing.

The pipeline for proteins analysis

Description of SAMEM user interface

Description of SAMEM data flow

SAMEM test results

SAMEM citation:

• Gunbin KV, Genaev MA, Afonnikov DA, Kolchanov NA. A computer system for the analysis of molecular evolution modes of protein-encoding genes (SAMEM): The relationship between molecular evolution and phenotypic traits. Moscow University Biological Sciences Bulletin. 2010 65(4):142-144. (First version of SAMEM)
• Gunbin KV, Suslov VV, Turnaev II, Afonnikov DA, Kolchanov NA. Molecular evolution of cyclin proteins in animals and fungi. BMC Evol Biol. 2011 Jul 28;11:224. (Algorithm for rare aminoacid replacements detection)
• Gunbin KV, Genaev MA, Turnaev II, Afonnikov DA. Computer system for analysis of molecular evolution modes of genes and proteins: a case study of the cyclin B molecular evolution. Tomsk State University Journal of Biology. 2011. N 4 (16). P. 170-184. (In Russian) (Russian citation)
• Gunbin KV, Suslov VV, Genaev MA, Afonnikov DA. Computer System for Analysis of Molecular Evolution Modes (SAMEM): Analysis of molecular evolution modes at deep inner branches of the phylogenetic tree. In Silico Biology. 2012. 11(2011/2012):109-123. (Most recent version of SAMEM; Algorithm for Kr/Kc calculation)
• Gunbin KV, Ruvinsky A. Evolution of General Transcription Factors. J Mol Evol. 2013 Feb;76(1-2):28-47 (Algorithm for rare aminoacid replacements detection)