vbguthrie edited this page Mar 15, 2018 · 10 revisions

NAPA - Network Analysis of Protein Adaptation

Karchin Lab, Institute of Computational Medicine, Johns Hopkins University.

Author: Violeta Beleva Guthrie

Contact: vbeleva at jhu dot edu

NAPA is a python package that performs network construction and analysis to investigate intra-protein residue coevolution. Network analysis is particularly useful in evaluating recent genetic evolution of novel functions resulting from multiple mutations that interact in a non-linear fashion. An example is the adaptation of β-lactamase to confer antibiotic resistance.

NAPA requires as input a multiple sequence alignment of related protein sequences undergoing adaptation. A phylogenetic tree or a tree ensemble based on the sequence alignment may also be provided as input. NAPA produces protein residue mutation networks (undirected for sequence alignment input; directed with phylogenetic tree input) and performs network analysis to assist with identification of sets of coevolving mutations that interact to improve protein function.

Contents

Install
Quick Start
Sample Data
Input Files
Results
FAQ
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Publications

Beleva-Guthrie V, Allen J, Camps M, and Karchin R (2011) Network models of TEM β-lactamase mutations coevolving under antibiotic selection show modular structure and anticipate evolutionary trajectories. PLoS Computational Biology. 7(9):e1002184. PubMed

Beleva Guthrie V, Masica DL, Fraser A, Federico J, Fan Y, Camps M, Karchin R (2018). Network Analysis of Protein Adaptation: modeling the functional impact of multiple mutations. Mol. Biol. Evo. Epub ahead of print | PubMed

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