PYCOEVOL: A Python workflow to study protein-protein coevolution

Protein coevolution has emerged as an important research topic. Several methods and scoring systems weredeveloped to quantify coevolution, though the quality of the results usually depends on the completeness ofthe biological data. To simplify the computation of coevolution indicators from the data, we haveimplemented a fully integrated and automated workflow which enables efficient analysis of proteincoevolution, using the Python scripting language. Pycoevol automates access to remote or local databasesand third-party applications, including also data processing functions. For a given protein complex understudy, Pycoevol retrieves and processes all the information needed to undergo the analysis, namelyhomologous sequence search, multiple sequence alignment computation and coevolution analysis, using aMutual Information indicator. In addition, friendly output results are created, namely histograms andheatmaps of inter-protein mutual information scores, as well as lists of significant coevolving residue pairs.An illustrative example is presented. Pycoevol is platform independent, and is available under the generalpublic license from http://code.google.com/p/pycoevol.