HSSP curve
Contents
Introduction to HSSP curve
HSSP is a derived database merging structural (3-D) and sequence (1-D) information. For each protein of known 3-D structure from the Protein Data Bank (PDB), the database has a multiple sequence alignment of all available homologues and a sequence profile characteristic of the family. The list of homologues is the result of a database search in SwissProt using a position-weighted dynamic programming method for sequence profile alignment (MaxHom). The database is updated frequently. The listed homologues are very likely to have the same 3-D structure as the PDB protein to which they have been aligned. As a result, the database is not only a database of aligned sequence families, but also a database of implied secondary and tertiary structures covering 29% of all SwissProt-stored sequences.
Existing visualisations
Tool Objective
Visualize the HSSP curve and allow the user to dynamically filter or categorize the data shown on the graph for better insights.
Core Functionalities
Task | Implemented |
---|---|
Import BLAST results | No |
Parse BLAST results | No |
Visualize HSSP curve | No |
Ability to filter based on a threshold | No |
People
References
http://en.wikipedia.org/wiki/Homology-derived_Secondary_Structure_of_Proteins
http://www.ncbi.nlm.nih.gov/pubmed/?term=UniqueProt%3A+creating+representative+protein+sequence+sets