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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. Optionally an ensemble of phylogenetic trees of the sequences may also be provided as input. NAPA produces residue mutation networks (undirected for sequence alignment input; directed with phylogenetic tree input) and network analysis products that assist with identification of sets of coevolving mutations that interact to confer function.
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