String Matching Input: Strings P (pattern) and T (text); |P| = m, |T| = n. Output: Indices of all occurrences of P in T. ExampleT = discombobulate later.

Slides:



Advertisements
Similar presentations
Parametrized Matching Amir, Farach, Muthukrishnan Orgad Keller.
Advertisements

© 2004 Goodrich, Tamassia Pattern Matching1. © 2004 Goodrich, Tamassia Pattern Matching2 Strings A string is a sequence of characters Examples of strings:
CS 208: Computing Theory Assoc. Prof. Dr. Brahim Hnich Faculty of Computer Sciences Izmir University of Economics.
Algorithm : Design & Analysis [19]
Designing Algorithms Csci 107 Lecture 4. Outline Last time Computing 1+2+…+n Adding 2 n-digit numbers Today: More algorithms Sequential search Variations.
Data Structures and Algorithms (AT70.02) Comp. Sc. and Inf. Mgmt. Asian Institute of Technology Instructor: Dr. Sumanta Guha Slide Sources: CLRS “Intro.
Yangjun Chen 1 String Matching String matching problem - prefix - suffix - automata - String-matching automata - prefix function - Knuth-Morris-Pratt algorithm.
Advanced Algorithm Design and Analysis (Lecture 4) SW5 fall 2004 Simonas Šaltenis E1-215b
Prefix & Suffix Example W = ab is a prefix of X = abefac where Y = efac. Example W = cdaa is a suffix of X = acbecdaa where Y = acbe A string W is a prefix.
1 Prof. Dr. Th. Ottmann Theory I Algorithm Design and Analysis (12 - Text search, part 1)
Pattern Matching1. 2 Outline and Reading Strings (§9.1.1) Pattern matching algorithms Brute-force algorithm (§9.1.2) Boyer-Moore algorithm (§9.1.3) Knuth-Morris-Pratt.
Goodrich, Tamassia String Processing1 Pattern Matching.
UMass Lowell Computer Science Analysis of Algorithms Prof. Karen Daniels Fall, 2006 Wednesday, 12/6/06 String Matching Algorithms Chapter 32.
6-1 String Matching Learning Outcomes Students are able to: Explain naïve, Rabin-Karp, Knuth-Morris- Pratt algorithms Analyse the complexity of these algorithms.
1 CSE 417: Algorithms and Computational Complexity Winter 2001 Lecture 15 Instructor: Paul Beame.
UMass Lowell Computer Science Analysis of Algorithms Prof. Karen Daniels Fall, 2001 Lecture 8 Tuesday, 11/13/01 String Matching Algorithms Chapter.
Boyer-Moore string search algorithm Book by Dan Gusfield: Algorithms on Strings, Trees and Sequences (1997) Original: Robert S. Boyer, J Strother Moore.
1 Finite Automata. 2 Finite Automaton Input “Accept” or “Reject” String Finite Automaton Output.
String Matching COMP171 Fall String matching 2 Pattern Matching * Given a text string T[0..n-1] and a pattern P[0..m-1], find all occurrences of.
1 Convolution and Its Applications to Sequence Analysis Student: Bo-Hung Wu Advisor: Professor Herng-Yow Chen & R. C. T. Lee Department of Computer Science.
Designing Algorithms Csci 107 Lecture 4.
Pattern Matching COMP171 Spring Pattern Matching / Slide 2 Pattern Matching * Given a text string T[0..n-1] and a pattern P[0..m-1], find all occurrences.
Raita Algorithm T. RAITA Advisor: Prof. R. C. T. Lee
Algorithms and Data Structures. /course/eleg67701-f/Topic-1b2 Outline  Data Structures  Space Complexity  Case Study: string matching Array implementation.
Pattern Matching1. 2 Outline Strings Pattern matching algorithms Brute-force algorithm Boyer-Moore algorithm Knuth-Morris-Pratt algorithm.
String Matching. Problem is to find if a pattern P[1..m] occurs within text T[1..n] Simple solution: Naïve String Matching –Match each position in the.
1 HEINZ NIXDORF INSTITUTE University of Paderborn Algorithms and Complexity Christian Schindelhauer Search Algorithms Winter Semester 2004/ Oct.
String Matching Chapter 32 Highlights Charles Tappert Seidenberg School of CSIS, Pace University.
KMP String Matching Prepared By: Carlens Faustin.
Advanced Algorithm Design and Analysis (Lecture 3) SW5 fall 2004 Simonas Šaltenis E1-215b
20/10/2015Applied Algorithmics - week31 String Processing  Typical applications: pattern matching/recognition molecular biology, comparative genomics,
String Matching Fundamental Data Structures and Algorithms April 22, 2003.
MCS 101: Algorithms Instructor Neelima Gupta
Application: String Matching By Rong Ge COSC3100
Strings and Pattern Matching Algorithms Pattern P[0..m-1] Text T[0..n-1] Brute Force Pattern Matching Algorithm BruteForceMatch(T,P): Input: Strings T.
1 HEINZ NIXDORF INSTITUTE University of Paderborn Algorithms and Complexity Christian Schindelhauer Search Algorithms Winter Semester 2004/ Oct.
MCS 101: Algorithms Instructor Neelima Gupta
String Searching CSCI 2720 Spring 2007 Eileen Kraemer.
String Matching String Matching Problem We introduce a general framework which is suitable to capture an essence of compressed pattern matching according.
Exact String Matching Algorithms Presented By Dr. Shazzad Hosain Asst. Prof. EECS, NSU.
1 String Matching Algorithms Topics  Basics of Strings  Brute-force String Matcher  Rabin-Karp String Matching Algorithm  KMP Algorithm.
CS5263 Bioinformatics Lecture 15 & 16 Exact String Matching Algorithms.
Fundamental Data Structures and Algorithms
String-Matching Problem COSC Advanced Algorithm Analysis and Design
1/39 COMP170 Tutorial 13: Pattern Matching T: P:.
CSC-305 Design and Analysis of AlgorithmsBS(CS) -6 Fall-2014CSC-305 Design and Analysis of AlgorithmsBS(CS) -6 Fall-2014 Design and Analysis of Algorithms.
String Searching 2 of 2. String search Simple search –Slide the window by 1 t = t +1; KMP –Slide the window faster t = t + s – M[s] –Never recheck the.
Rabin & Karp Algorithm. Rabin-Karp – the idea Compare a string's hash values, rather than the strings themselves. For efficiency, the hash value of the.
Fall 2004COMP 3351 Finite Automata. Fall 2004COMP 3352 Finite Automaton Input String Output String Finite Automaton.
1 String Matching Algorithms Mohd. Fahim Lecturer Department of Computer Engineering Faculty of Engineering and Technology Jamia Millia Islamia New Delhi,
CSG523/ Desain dan Analisis Algoritma
Finite State Machines Dr K R Bond 2009
Advanced Algorithms Analysis and Design
Advanced Algorithms Analysis and Design
String Matching (Chap. 32)
13 Text Processing Hongfei Yan June 1, 2016.
Rabin & Karp Algorithm.
CSE322 Finite Automata Lecture #2.
Tuesday, 12/3/02 String Matching Algorithms Chapter 32
String-Matching Algorithms (UNIT-5)
Pattern Matching 12/8/ :21 PM Pattern Matching Pattern Matching
Pushdown Automaton (PDA)
Pattern Matching 1/14/2019 8:30 AM Pattern Matching Pattern Matching.
KMP String Matching Donald Knuth Jim H. Morris Vaughan Pratt 1997.
Pattern Matching 2/15/2019 6:17 PM Pattern Matching Pattern Matching.
Data Structures and Algorithms (AT70. 02) Comp. Sc. and Inf. Mgmt
Pattern Matching Pattern Matching 5/1/2019 3:53 PM Spring 2007
Pattern Matching 4/27/2019 1:16 AM Pattern Matching Pattern Matching
Sequences 5/17/ :43 AM Pattern Matching.
Non Deterministic Automata
Presentation transcript:

String Matching Input: Strings P (pattern) and T (text); |P| = m, |T| = n. Output: Indices of all occurrences of P in T. ExampleT = discombobulate later 15 > |T| (no occurrence of P) P output combo 4 (i.e., with shift 3) ate 12

Applications Text retrieval Computational biology - DNA is a one-dimensional (1-D) string of characters A’s, G’s, C’s, T’s. Searching for DNA patterns Comparing two or more DNA strings for similarities Reconstructing DNA strings from overlapping fragments. - All information for 3-D protein folding is contained in protein sequence itself and independent of the environment.

Sliding the Pattern Template T = b i o l o g y P = l o g i c n = 7 m = 5 b i o l o g y l o g i c b i o l o g y l o g i c b i o l o g y l o g i c b i o l o g y l o g i c b i o l o g y l o g i c b i o l o g y l o g i c T[1]  P[1] T[4] = P[1], T[5] = P[2], T[6] = P[3], but T[7]  P[4] T[2]  P[1] b i o l o g y l o g i c No match! T[3]  P[1]

Another Example T = b i o l o g i c a l P = l o g i c n = 10 m = 5 b i o l o g i c a l l o g i c Match found! return 4.

The Naive Matcher Pattern: P[1..m] Text: T[1..n] Naive-String-Matcher(T, P) // find all occurrences of P in T. for s = 1 to n  m +1 do if P[1.. m] = T[s.. s+m  1] then print “Pattern occurs at index” s T:T: P:P: s s+m-1 1 m

Time Complexity m(n  m + 1) comparisons (as below) in the worst case. m chars P T n  m+1 n n  m + 1 blocks, each requiring m comparisons Time complexity is O(mn)!

Finite Automaton A finite automaton consists of a finite set Q of states a start state a set A of accepting states a finite input alphabet  a transition function d : Q    Q. a 01 b a b start state accepting state Example a b 0 1 state input transition function

Accepting a String a 01 b a b aabba bbabb input state sequence accepts? Yes No Always begins at the start state. Accepts a string if it ends at an accepting state after accepting all string chars. Otherwise, it rejects the string.

A String Matching Automaton Pattern P = a a b a a b P a a b a input state T = a b b a a a b a a b a state sequence a b b a b a b a a b Pattern occurs at indices 5 and 8! aba not rescanned due to transition 4  2 Ex

Key Ideas of Automaton Matching Do not rescan chars of T that have already been examined. Slide pattern forward by more than one position if possible.

The Automaton Matcher Finite-Automaton-Matcher(T, d, m) n = length[T] q = 0 // current state for i = 1 to n do q = d(q, T[i]) // d function precomputed if q = m // match succeeds then print “Pattern occurs at index” i  m+1 O(n) if the state transition function d is available. But computing d requires O(m |  |)! // details omitted. 3