OrthoWeb – web application for macro- and microevolutionary analysis of genes

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Zakhar Mustafin, Alexey Mukhin, Dmitry Afonnikov, Yury Matushkin, Sergey Lashin¹
¹Kurchatov Genomics Center, ICG SB RAS, Novosibirsk, Russia, mustafinzs@bionet.nsc.ru

Problems of macro- and microevolution remain key problems of biology. Phylostratigraphic analysis became one of the most popular methods for studying macroevolutionary characteristic of genes. It is based on estimation of the divergence time among orthologous genes. Along with methods of microevolutionary analysis (for example, dN/dS ratio estimation), phylostratigraphic methods are increasingly included into the methodological arsenal of evolutionary bioinformatics. There are some software packages used for computational analysis of the evolution by using different phylostratigraphic and microevolutionary indices, but they require users to know some additional software or programming languages. Here we present OrthoWeb software to calculate such indices using web browser only.

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Yana Sizentsova

3 years ago

Thank you for the interesting topic. I do not quite understand what the PAI index and what it shows. Could you clarify this?

Zakhar Mustafin

Reply to Yana Sizentsova

Thank you for the question.
The PAI index is a numerical representation of the gene age. So PAI shows the level of the last common ancestor node in the whole taxonomic tree, containing at least one species from the list of species possessing orthologs of a gene under analysis.
It helps to find “ancient” genes, orphan genes and some other interesting targets to more precise analysis.