The server builds multiple sequence codon-based alignments, calculates the ratio of silent to replacement nucleotide substitution rates (dN/dS), determine the rate of sequence evolution in a phylogenetic context. In contrast to other tools OMEGAbase is not limited to pairwise analyses; it is designed to analyze orthologous gene sets (n>2) between several species enabling the assessment of selective constraint of each lineage in comparison to the rest of the phylogenetic tree. The server is designed to run in batch mode analysis with up to 100 sets of orthologous sequences that can be submitted at the same time.

→ Enter OMEGAbase to compute personal datasets

A total of >100,000 pre-computed values of selective pressure are stored in OMEGAbase, consisting in the core set of 10,573 orthologous genes among 10 mammalian species (Human, Chimpanzee, Orang-utang, Macaque, Marmoset, Mouse, Rat, Dog, Cow, Horse). Results have been obtained with the codeml program from the PAML5 package (Branch-site test as set as model=2, NSsites=2) [see theoretical principles] .

Entries are:
• Selective pressure type

→ positive selection
→ negative/neutral selection

• Specificity of selection

→ lineage-specific positive selection
→ Shared (co-occurency) positive selection among lineages

• Proportion of sites under positive selection

→ Number of positive selected sites (codon)
→ Similarity or difference of positive selected sites between PSG among lineages

• Identification of sites under positive selection

→ Codon and position identification of positive selected sites (codon)

→ Enter OMEGAbase to query pre-computed datasets