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Authors: Fábio Madeira and Ludwig Krippahl

Affiliation: Universidade Nova de Lisboa, Portugal

ISBN: 978-989-8425-90-4

Keyword(s): Protein coevolution, Multiple sequence alignments, Mutual information.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering ; Data Mining and Machine Learning ; Sequence Analysis

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 of sig nificant coevolving residue pairs. An illustrative example is presented. Pycoevol is platform independent, and is available under the general public license from http://code.google.com/p/pycoevol. (More)

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Paper citation in several formats:
Madeira, F.; Madeira, F. and Krippahl, L. (2012). PYCOEVOL - A Python Workflow to Study Protein-protein Coevolution.In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012) ISBN 978-989-8425-90-4, pages 143-149. DOI: 10.5220/0003737901430149

@conference{bioinformatics12,
author={Fábio Madeira. and Fábio Madeira. and Ludwig Krippahl.},
title={PYCOEVOL - A Python Workflow to Study Protein-protein Coevolution},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)},
year={2012},
pages={143-149},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003737901430149},
isbn={978-989-8425-90-4},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)
TI - PYCOEVOL - A Python Workflow to Study Protein-protein Coevolution
SN - 978-989-8425-90-4
AU - Madeira, F.
AU - Madeira, F.
AU - Krippahl, L.
PY - 2012
SP - 143
EP - 149
DO - 10.5220/0003737901430149

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