Intro - Computational Molecular Biology Introduction and...

Info iconThis preview shows pages 1–16. Sign up to view the full content.

View Full Document Right Arrow Icon
Computational Molecular Biology Introduction and Preliminaries
Background image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
My T. Thai mythai@cise.ufl.edu 2 Preliminaries in Computer Science Strings and alphabet Basic notations in graph theory Algorithms and Complexity
Background image of page 2
My T. Thai mythai@cise.ufl.edu 3 Strings Consist of a sequence of letters: DNA: four nucleotides A, C, G, T Proteins: 20 symbol alphabet of animo acids Given a string s , we have the following notations: Length: | s | Substring: ACT is a substring of ATGACTG Superstring: ATGACTG is a superstring of ACT Index and interval: s [ i ] and s [ i..j ] Prefix and suffix: s [ 1..j ] and s [ i.. | s |]
Background image of page 3

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
My T. Thai mythai@cise.ufl.edu 4 Graphs G = (V, E) where V is a set of vertices and E is a set of edges Undirected graph: edges are undirected Directed graph: edges are directed Weighted graph G = (V, E, w ) where each edge has some weight Some special graphs: complete graph, bipartite graph, tree, and interval graph Subgraph, spanning tree, steiner tree
Background image of page 4
My T. Thai mythai@cise.ufl.edu 5 Interval Graphs Intersection graph of a set of intervals on the real line A vertex represents an interval and an edge (u, v) exists if intervals u and v intersect
Background image of page 5

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
My T. Thai mythai@cise.ufl.edu 6 Some Problems in Graphs Euler circuit : Given a graph, find a cycle that passes through each edge exactly once Hamiltonian circuit : Given a graph, find a cycle that passes through each vertex exactly once Minimum Spanning Tree : Given a weighted undirected graph, find a spanning tree with minimum total weight Maximum Matching : Given an undirected graph, find a maximum cardinality matching, which is a subset of edges such that no two edges in the subset share an endpoint
Background image of page 6
My T. Thai mythai@cise.ufl.edu 7 P vs. NP Class of P : Set of problems solvable by polynomial-time algoirthms Class of NP : Set of problems whose solutions, once found, can be verified in polynomial time NP-complete (NP-hard) problems : cannot obtain an optimal solutions in polynomial time
Background image of page 7

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
My T. Thai mythai@cise.ufl.edu 8 Some approaches for NP-complete Problems Special-case method : Work on the problem with a restricted class of inputs Exhaustive search : Design an exponential-time algorithms that may perform well in practice Approximation algorithms : Design a polynomial- time algorithm that is guaranteed to find near-optimal solutions (with a good approximation ratio) Heuristics : Fast algorithms that produce satisfactory solutions most of the time but without guarantee
Background image of page 8
My T. Thai mythai@cise.ufl.edu 9 Preliminaries in Molecular Biology
Background image of page 9

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
My T. Thai mythai@cise.ufl.edu 10 DNA and Base Pairs Double helix consisting of two dual strands Has four types of nucleotides: Adenine, Thymine, Guanine, Cytosine Base Pairs: A↔T , C↔G Two ends of a strand are marked with 3 and 5 The entire DNA of a living organism is called its genome
Background image of page 10
My T. Thai mythai@cise.ufl.edu 11 DNA Sequences
Background image of page 11

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
My T. Thai mythai@cise.ufl.edu 12 DNA Replication Strands are separated Each strand is replicated using one of the parental strands as a template
Background image of page 12
My T. Thai mythai@cise.ufl.edu 13 Cell, Chromosome, and DNA
Background image of page 13

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
My T. Thai mythai@cise.ufl.edu 14 Cell Classification
Background image of page 14
My T. Thai
Background image of page 15

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Image of page 16
This is the end of the preview. Sign up to access the rest of the document.

Page1 / 44

Intro - Computational Molecular Biology Introduction and...

This preview shows document pages 1 - 16. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online