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PYCOEVOL: A Python workflow to study protein-protein coevolution
February 2012
bioinf12
Protein coevolution has emerged as an important research topic. Several methods and scoring systems were developed to quantify coevolution, though the quality of the results usually depends on the completeness of the biological data. To simplify the computation of coevolution indicators from the data, we have implemented a fully integrated and automated workflow which enables efficient analysis of protein coevolution, using the Python scripting language. Pycoevol automates access to remote or local databases and third-party applications, including also data processing functions. For a given protein complex under study, Pycoevol retrieves and processes all the information needed to undergo the analysis, namely homologous sequence search, multiple sequence alignment computation and coevolution analysis, using a Mutual Information indicator. In addition, friendly output results are created, namely histograms and heatmaps of inter-protein mutual information scores, as well as lists...
In proceedings
Fábio Madeira, Ludwig Krippahl
Jan Schier
BIOSTEC 2012: 5th International Joint Conference on Biomedical Engineering Systems and Technologies
BIOINFORMATICS 2012: International Conference on Bioinformatics Models, Methods and Algorithms - Proceedings
INSTICC Press
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143-149
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Fábio Madeira and Ludwig Krippahl, PYCOEVOL: A Python workflow to study protein-protein coevolution, in: Jan Schier (eds), BIOSTEC 2012: 5th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOINFORMATICS 2012: International Conference on Bioinformatics Models, Methods and Algorithms - Proceedings, INSTICC Press, Pag. 143-149, February 2012.
<a href="/people/members/view.php?code=46d17da71ed1c44fe2fd9b6ad9321cec" class="author">Fábio Madeira</a> and <a href="/people/members/view.php?code=195d68ea5904b58472fd8c8aedcae233" class="author">Ludwig Krippahl</a>, <b>PYCOEVOL: A Python workflow to study protein-protein coevolution</b>, in: Jan Schier (eds), <u>BIOSTEC 2012: 5th International Joint Conference on Biomedical Engineering Systems and Technologies</u>, BIOINFORMATICS 2012: International Conference on Bioinformatics Models, Methods and Algorithms - Proceedings, <a href="http://www.insticc.net/" title="Link to external entity..." target="_blank" class="publisher">INSTICC Press</a>, Pag. 143-149, February 2012.
@inproceedings {bioinf12, author = {F{\'a}bio Madeira and Ludwig Krippahl}, editor = {Jan Schier}, title = {PYCOEVOL: A Python workflow to study protein-protein coevolution}, booktitle = {BIOSTEC 2012: 5th International Joint Conference on Biomedical Engineering Systems and Technologies}, series = {BIOINFORMATICS 2012: International Conference on Bioinformatics Models, Methods and Algorithms - Proceedings}, publisher = {INSTICC Press}, pages = {143-149}, abstract = {Protein coevolution has emerged as an important research topic. Several methods and scoring systems were developed to quantify coevolution, though the quality of the results usually depends on the completeness of the biological data. To simplify the computation of coevolution indicators from the data, we have implemented a fully integrated and automated workflow which enables efficient analysis of protein coevolution, using the Python scripting language. Pycoevol automates access to remote or local databases and third-party applications, including also data processing functions. For a given protein complex under study, Pycoevol retrieves and processes all the information needed to undergo the analysis, namely homologous sequence search, multiple sequence alignment computation and coevolution analysis, using a Mutual Information indicator. In addition, friendly output results are created, namely histograms and heatmaps of inter-protein mutual information scores, as well as lists...}, month = {February}, year = {2012}, }
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