Presentation on theme: "Robert Fraser May 21, 2010. Outline Contact Maps Pattern Matching in Matrices Adaptive Analysis Experimental Results Conclusions, Future Work."— Presentation transcript:
Robert Fraser May 21, 2010
Outline Contact Maps Pattern Matching in Matrices Adaptive Analysis Experimental Results Conclusions, Future Work
Contact Maps An abstract translational and rotational invariant representation of a proteins topology An N × N matrix C, where N is the number of amino acids in the given protein Entry C ij is a boolean, indicating whether amino acid i is in contact with amino acid j. Hippy Demo
Pattern Matching in Matrices Search for pattern: In large text:
Adaptive Analysis Idea came from sorting: Some sequences are easier to sort than others
Contact maps Shouldnt search where you wont find a relevant match: Eliminate areas along the central axis Eliminate areas that are not in secondary structures
Which technique is best......depends upon the characteristics of your pattern.
Conclusions Significant gains may be achieved by incorporating additional information into your search. Linear search performs best if you restrict the search to the interface region of a contact map. Future work: further exploiting the characteristics of the data to improve search time: i.e. The matrices are sparse!