PANADA: Protein Association Network Annotation, Determination and Analysis

Alberto J. M. Martin, Ian Walsh, Tomás Di Domenico, Ivan Mičetić, Silvio C. E. Tosatto, Elena Papaleo
2013 PLoS ONE  
Increasingly large numbers of proteins require methods for functional annotation. This is typically based on pairwise inference from the homology of either protein sequence or structure. Recently, similarity networks have been presented to leverage both the ability to visualize relationships between proteins and assess the transferability of functional inference. Here we present PANADA, a novel toolkit for the visualization and analysis of protein similarity networks in Cytoscape. Networks can
more » ... e constructed based on pairwise sequence or structural alignments either on a set of proteins or, alternatively, by database search from a single sequence. The Panada web server, executable for download and examples and extensive help files are available at URL: http://protein.bio.unipd.it/panada/.
doi:10.1371/journal.pone.0078383 pmid:24265686 pmcid:PMC3827049 fatcat:32qvawdtjngp5onz5of7rgn3ee