title: PANADA: protein association network annotation, determination and analysis.
abstract: 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 be 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/.
authors.affiliation: Department of Biology, University of Padova, Padova, Italy.
authors.forename: Alberto J M
authors.initials: AJ
authors.lastname: Martin
authors.forename: Ian
authors.initials: I
authors.lastname: Walsh
authors.forename: Tomás Di
authors.initials: TD
authors.lastname: Domenico
authors.forename: Ivan
authors.initials: I
authors.lastname: Mičetić
authors.forename: Silvio C E
authors.initials: SC
authors.lastname: Tosatto
mesh_terms: D003196:Computer Graphics; D020407:Internet; D058977:Molecular Sequence Annotation / Q000379:methods*; D025941:Protein Interaction Mapping / Q000379:methods*; D016415:Sequence Alignment; D012984:Software