Pythoscape: a framework for generation of large protein similarity networks

Abstract

Pythoscape is a framework implemented in Python for processing large protein similarity networks for visualization in other software packages. Protein similarity networks are graphical representations of sequence, structural and other similarities among proteins for which pairwise all-by-all similarity connections have been calculated. Mapping of biological and other information to network nodes or edges enables hypothesis creation about sequence-structure-function relationships across sets of related proteins. Pythoscape provides several options to calculate pairwise similarities for input sequences or structures, applies filters to network edges and defines sets of similar nodes and their associated data as single nodes (termed representative nodes) for compression of network information and output data or formatted files for visualization.

Fig. 1.

Sequence similarity network of the GST superfamily generated by Pythoscape and visualized in Cytoscape. To compact the view for this figure, networks were layed out using the organic layout in Cytoscape rather than the distances computed from a similarity metric. In all, 664 representative nodes are used to describe pairwise relationships among 7447 sequences. (A) Representative network with functional classes colored, if annotated by SwissProt in a family (The UniProt Consortium, 2011). Family membership is indicated if one or more sequences in the abstracted node are associated with that family. (B) Full non-abstracted network for the group of GSTs found mostly in eukaryotes (boxed in A)