String Processing.

Slides:



Advertisements
Similar presentations
Chapter 7 Space and Time Tradeoffs Copyright © 2007 Pearson Addison-Wesley. All rights reserved.
Advertisements

Dynamic Programming Nithya Tarek. Dynamic Programming Dynamic programming solves problems by combining the solutions to sub problems. Paradigms: Divide.
Space-for-Time Tradeoffs
Inexact Matching of Strings General Problem –Input Strings S and T –Questions How distant is S from T? How similar is S to T? Solution Technique –Dynamic.
15-853Page : Algorithms in the Real World Suffix Trees.
296.3: Algorithms in the Real World
Tries Search for ‘bell’ O(n) by KMP algorithm O(dm) in a trie Tries
Boyer Moore Algorithm String Matching Problem Algorithm 3 cases Searching Timing.
1 Prof. Dr. Th. Ottmann Theory I Algorithm Design and Analysis (12 - Text search, part 1)
Design and Analysis of Algorithms - Chapter 71 Space-time tradeoffs For many problems some extra space really pays off (extra space in tables - breathing.
Goodrich, Tamassia String Processing1 Pattern Matching.
6/11/2015 © Bud Mishra, 2001 L7-1 Lecture #7: Local Alignment Computational Biology Lecture #7: Local Alignment Bud Mishra Professor of Computer Science.
1 Query Languages. 2 Boolean Queries Keywords combined with Boolean operators: –OR: (e 1 OR e 2 ) –AND: (e 1 AND e 2 ) –BUT: (e 1 BUT e 2 ) Satisfy e.
UNIVERSITY OF SOUTH CAROLINA College of Engineering & Information Technology Bioinformatics Algorithms and Data Structures Chapter 11 sections4-7 Lecturer:
Boyer-Moore Algorithm 3 main ideas –right to left scan –bad character rule –good suffix rule.
Dynamic Text and Static Pattern Matching Amihood Amir Gad M. Landau Moshe Lewenstein Dina Sokol Bar-Ilan University.
Sequence Alignment Variations Computing alignments using only O(m) space rather than O(mn) space. Computing alignments with bounded difference Exclusion.
This material in not in your text (except as exercises) Sequence Comparisons –Problems in molecular biology involve finding the minimum number of edit.
Designing Algorithms Csci 107 Lecture 4.
Chapter 7 Space and Time Tradeoffs Copyright © 2007 Pearson Addison-Wesley. All rights reserved.
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.
Algorithms and Data Structures. /course/eleg67701-f/Topic-1b2 Outline  Data Structures  Space Complexity  Case Study: string matching Array implementation.
Aho-Corasick Algorithm Generalizes KMP to handle sets of strings New ideas –keyword trees –failure functions/links –output links.
1 Exact Matching Charles Yan Na ï ve Method Input: P: pattern; T: Text Output: Occurrences of P in T Algorithm Naive Align P with the left end.
1 Theory I Algorithm Design and Analysis (11 - Edit distance and approximate string matching) Prof. Dr. Th. Ottmann.
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.
Space-Efficient Sequence Alignment Space-Efficient Sequence Alignment Bioinformatics 202 University of California, San Diego Lecture Notes No. 7 Dr. Pavel.
KMP String Matching Prepared By: Carlens Faustin.
Chapter 7 Space and Time Tradeoffs James Gain & Sonia Berman
Boyer Moore Algorithm Idan Szpektor. Boyer and Moore.
MCS 101: Algorithms Instructor Neelima Gupta
Application: String Matching By Rong Ge COSC3100
1 Chapter 6 Dynamic Programming. 2 Algorithmic Paradigms Greedy. Build up a solution incrementally, optimizing some local criterion. Divide-and-conquer.
Book: Algorithms on strings, trees and sequences by Dan Gusfield Presented by: Amir Anter and Vladimir Zoubritsky.
MCS 101: Algorithms Instructor Neelima Gupta
ICS220 – Data Structures and Algorithms Analysis Lecture 14 Dr. Ken Cosh.
1/39 COMP170 Tutorial 13: Pattern Matching T: P:.
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.
CSG523/ Desain dan Analisis Algoritma
15-853:Algorithms in the Real World
COMP261 Lecture 20 String Searching 2 of 2.
@#? Text Search g ~ A R B n f u j u q e ! 4 k ] { u "!"
Tries 9/14/ :13 AM Presentation for use with the textbook Data Structures and Algorithms in Java, 6th edition, by M. T. Goodrich, R. Tamassia, and.
13 Text Processing Hongfei Yan June 1, 2016.
JinJu Lee & Beatrice Seifert CSE 5311 Fall 2005 Week 10 (Nov 1 & 3)
String Processing.
Fast Fourier Transform
Knuth-Morris-Pratt algorithm
Space-for-time tradeoffs
Tuesday, 12/3/02 String Matching Algorithms Chapter 32
Knuth-Morris-Pratt KMP algorithm. [over binary alphabet]
String-Matching Algorithms (UNIT-5)
Chapter 7 Space and Time Tradeoffs
Pattern Matching 12/8/ :21 PM Pattern Matching Pattern Matching
Pattern Matching 1/14/2019 8:30 AM Pattern Matching Pattern Matching.
KMP String Matching Donald Knuth Jim H. Morris Vaughan Pratt 1997.
Space-for-time tradeoffs
Pattern Matching 2/15/2019 6:17 PM Pattern Matching Pattern Matching.
Tries 2/23/2019 8:29 AM Tries 2/23/2019 8:29 AM Tries.
Suffix Trees String … any sequence of characters.
Space-for-time tradeoffs
Tries 2/27/2019 5:37 PM Tries Tries.
Knuth-Morris-Pratt Algorithm.
Pattern Matching Pattern Matching 5/1/2019 3:53 PM Spring 2007
Space-for-time tradeoffs
Pattern Matching 4/27/2019 1:16 AM Pattern Matching Pattern Matching
Lecture 5 Dynamic Programming
Space-for-time tradeoffs
Sequences 5/17/ :43 AM Pattern Matching.
15-826: Multimedia Databases and Data Mining
Presentation transcript:

String Processing

Basic String Techniques Storing strings Reading text input by line Concatenating strings Checking for matching string at beginning Finding a substring within a larger string Counting occurrances in a string (e.g. how many vowels) Tokenizing: splitting a string into substrings by delimiters Sorting an array of strings

String Matching Find occurrences of T (length m) inside S (length n) Basic matching can use library functions Requires reasonably small strings Longer matching: naïve approach Loop over S (1 to n) Check whether T occurs starting at that point (1 to m) So, O(nm) total Better: Knuth-Morris-Pratt (KMP) Algorithm

Knuth-Morris-Pratt (KMP) Algorithm Idea: preprocess T (the one to find) – use matches there to know where to start the next match Preprocess: For character i in T, If the string matched to character i, but not to character i+1, Then, how many characters of the string preceding character i+1 match the beginning of the string to match This tells you where to start matching again Match like naïve. But, when you stop getting a match: Go back the given number of spaces (based on preprocess) Start match there

KMP Algorithm - running Example: T is abracadabra This says that if there is a match up until that character, but NOT that character, how many characters match in the beginning of the string. e.g. if the “c” is the first not to match, it means that the string had “abra” at the beginning. That means that we can restart here, assuming 1 character (the “a”, which comes right before the “c” matches. Could represent differently – where the # stored is the number matching the prefix, but then need to offset everything else by 1 Example we will use: S is abrabracabracadabracadabra a b r c d 1 2 3

a b r c d 1 2 3 i: 01234 S: abrabracabracadabracadabra T: abracadabra j: 01234 Mismatch at slot 4 (i=4, j=4). Back table has value 1 there. So, next we’ll continue with i=4, but j will go back to 1.

a b r c d 1 2 3 i: 0123456789 S: abrabracabracadabracadabra T: abracadabra j: 0123456 Mismatch at slot j=6 (and i=9). Back table has value 1 there. So, next we’ll continue with i=9, but j will go back to slot 1:

a b r c d 1 2 3 i: 0123456789012345678 S: abrabracabracadabracadabra T: abracadabra j: 01234567890 Full match here. Mark as found (at slot 8). Next one starts 4 back (i=18, j=4).

a b r c d 1 2 3 i: 01234567890123456789012345 S: abrabracabracadabracadabra T: abracadabra j: 01234567890 Full match here again. Mark as found (at slot 15). Next one would start 4 back (i=21).

Dynamic Programming on Strings Edit Distance: Given two strings, how many edits (insert space, delete digit, or have mismatch) are needed between them? Use DP: String A[1..n], B[1..m]: For A[1..i], B[1..j], we have V(i,j) = edit distance for substrings. We want V(n,m) V(0,0) = 0 V(i,0) = penalty to delete all i elements from A V(0,j) = penalty to delete all j elements from B V(i,j) = max: V(i-1,j-1) + score(A[i],B[i]) V(i-1,j)+score(A[i],-) V(i,j-1)+score(-,B[j]) Where score(A[i],B[j]) = 2 if matching, -1 if nonmatching, and score(x,-)=score(-,x) = -1 (penalty to delete = penalty to add a space)

More DP on Strings For Longest Common Subsequence Same as String Alignment Penalty for mismatch = infinity Penalty for add/delete = 0 Points for match = 1