Related Experiment Video
Updated: Aug 16, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Integrated graphical analysis of protein sequence features predicted from sequence composition
1Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden. Erik.Sonnhammer@cgb.ki.se
Abstract:
Several protein sequence analysis algorithms are based on properties of amino acid composition and repetitiveness. These include methods for prediction of secondary structure elements, coiled-coils, transmembrane segments or signal peptides, and for assignment of low-complexity, nonglobular, or intrinsically unstructured regions. The quality of such analyses can be greatly enhanced by graphical software tools that present predicted sequence features together in context and allow judgment to be focused simultaneously on several different types of supporting information. For these purposes, we describe the SFINX package, which allows many different sets of segmental or continuous-curve sequence feature data, generated by individual external programs, to be viewed in combination alongside a sequence dot-plot or a multiple alignment of database matches. The implementation is currently based on extensions to the graphical viewers Dotter and Blixem and scripts that convert data from external programs to a simple generic data definition format called SFS. We describe applications in which dot-plots and flanking database matches provide valuable contextual information for analyses based on compositional and repetitive sequence features. The system is also useful for comparing results from algorithms run with a range of parameters to determine appropriate values for defaults or cutoffs for large-scale genomic analyses.
More Related Videos
Related Concept Videos
Protein and Protein Structure
A protein's shape is critical to its function. For example, an enzyme can...
Conservation of Protein Domains Over Different Proteins
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein-protein Interfaces
Protein Networks
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Conservation of Protein Domains
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein-Protein Interfaces

