The 7 Bridges in Konigsberg and Compositional Representation 7桥在哥尼斯堡与成分的表征.pptVIP

The 7 Bridges in K?nigsberg and Compositional Representation of Protein Sequences Bailin Hao (郝柏林) (ITP BGI, CAS ) Huimin Xie (谢惠民) （Math Dept. Suzhou U） Shuyu Zhang (张淑誉) (IP. Acad. Sinica) Compositional Approach inProkaryote Phylogeny Justification of using K-tuples instead of primary protein sequences. Problem of uniqueness of reconstruction of protein sequence from its constituent K-tuples. Picking up a special class of proteins without biological knowledge. 7 bridges in K?nigsberg Basic Notions A Graph G=(V, E), where V is a set of nodes (vertices), E is a set of edges (bonds) Edges: undirected (u,v)=(v,u), uand v adjacent; directed (u,v) differs from (v,u), u incident to v. A weight may be associated with (u,v): cost, distance, transfer function, reaction rate, etc. Eulerian graph: each edge appears once and only once in a path Hamiltonian graph: each vertex appears once and only once in a path. Hamiltonian cycle of minimal weight --- Travel Salesman Problem (TSP) An Euler path: An Euler loop: Euler grahp: ? loop Semi-Euler praph: ? path, no loop Problem of Eulerian loop: simple, known solutions Problem of Hamiltonian paths: much harder Hamiltonian Loops: much harder 10 nodes 15 arcs di=3 ? nodes Traveling Salesman Problem NP-hard problems Graph = nodes + arcs Directed , Labeled arcs and nodes Simple graph: No rings at nodes: No repeated arcs: Indegree din(i) Outdegree dout(i) Euler graph: din(i) = dout(i) ? di ?i Simple Euler GraphDiagonal matrix: M=diag( d1, d2, … dn )Adjacent matrix: A={aij} aij=  aii= 0 Kirchhoff matrix: C=M-A