About this Course
4.5
460 ratings
94 reviews
World and internet is full of textual information. We search for information using textual queries, we read websites, books, e-mails. All those are strings from the point of view of computer science. To make sense of all that information and make search efficient, search engines use many string algorithms. Moreover, the emerging field of personalized medicine uses many search algorithms to find disease-causing mutations in the human genome....
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Flexible deadlines

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Intermediate Level

Intermediate Level

Clock

Suggested: 4 weeks of study, 4-8 hours/week

Approx. 18 hours to complete
Comment Dots

English

Subtitles: English

Skills you will gain

Suffix TreeSuffix ArrayKnuth–Morris–Pratt (KMP) AlgorithmAlgorithms On Strings
Globe

100% online courses

Start instantly and learn at your own schedule.
Calendar

Flexible deadlines

Reset deadlines in accordance to your schedule.
Intermediate Level

Intermediate Level

Clock

Suggested: 4 weeks of study, 4-8 hours/week

Approx. 18 hours to complete
Comment Dots

English

Subtitles: English

Syllabus - What you will learn from this course

1

Section
Clock
4 hours to complete

Suffix Trees

How would you search for a longest repeat in a string in LINEAR time? In 1973, Peter Weiner came up with a surprising solution that was based on suffix trees, the key data structure in pattern matching. Computer scientists were so impressed with his algorithm that they called it the Algorithm of the Year. In this lesson, we will explore some key ideas for pattern matching that will - through a series of trials and errors - bring us to suffix trees....
Reading
5 videos (Total 27 min), 5 readings, 1 quiz
Video5 videos
Brute Force Approach to Pattern Matching2m
Herding Patterns into Trie5m
Herding Text into Suffix Trie6m
Suffix Trees4m
Reading5 readings
Trie Construction - Pseudocode10m
FAQ10m
Slides and External References10m
Available Programming Languages10m
FAQ on Programming Assignments10m

2

Section
Clock
4 hours to complete

Burrows-Wheeler Transform and Suffix Arrays

Although EXACT pattern matching with suffix trees is fast, it is not clear how to use suffix trees for APPROXIMATE pattern matching. In 1994, Michael Burrows and David Wheeler invented an ingenious algorithm for text compression that is now known as Burrows-Wheeler Transform. They knew nothing about genomics, and they could not have imagined that 15 years later their algorithm will become the workhorse of biologists searching for genomic mutations. But what text compression has to do with pattern matching??? In this lesson you will learn that the fate of an algorithm is often hard to predict – its applications may appear in a field that has nothing to do with the original plan of its inventors....
Reading
5 videos (Total 30 min), 4 readings, 1 quiz
Video5 videos
Inverting Burrows-Wheeler Transform7m
Using BWT for Pattern Matching6m
Suffix Arrays5m
Approximate Pattern Matching6m
Reading4 readings
Using BWT for Pattern Matching10m
Pattern Matching with Suffix Array10m
FAQ10m
Slides and External References10m

3

Section
Clock
3 hours to complete

Knuth–Morris–Pratt Algorithm

Congratulations, you have now learned the key pattern matching concepts: tries, suffix trees, suffix arrays and even the Burrows-Wheeler transform! However, some of the results Pavel mentioned remain mysterious: e.g., how can we perform exact pattern matching in O(|Text|) time rather than in O(|Text|*|Pattern|) time as in the naïve brute force algorithm? How can it be that matching a 1000-nucleotide pattern against the human genome is nearly as fast as matching a 3-nucleotide pattern??? Also, even though Pavel showed how to quickly construct the suffix array given the suffix tree, he has not revealed the magic behind the fast algorithms for the suffix tree construction!In this module, Miсhael will address some algorithmic challenges that Pavel tried to hide from you :) such as the Knuth-Morris-Pratt algorithm for exact pattern matching and more efficient algorithms for suffix tree and suffix array construction....
Reading
5 videos (Total 35 min), 2 readings, 1 quiz
Video5 videos
Safe Shift3m
Prefix Function7m
Computing Prefix Function9m
Knuth-Morris-Pratt Algorithm5m
Reading2 readings
Programming Assignment 3 lasts for two weeksm
Slides and External References10m
Quiz1 practice exercise
Exact Pattern Matching30m

4

Section
Clock
5 hours to complete

Constructing Suffix Arrays and Suffix Trees

In this module we continue studying algorithmic challenges of the string algorithms. You will learn an O(n log n) algorithm for suffix array construction and a linear time algorithm for construction of suffix tree from a suffix array. You will also implement these algorithms and the Knuth-Morris-Pratt algorithm in the last Programming Assignment in this course....
Reading
11 videos (Total 76 min), 5 readings, 2 quizzes
Video11 videos
General Strategy6m
Initialization9m
Sort Doubled Cyclic Shifts8m
SortDouble Implementation6m
Updating Classes8m
Full Algorithm3m
Suffix Array and Suffix Tree8m
LCP Array5m
Computing the LCP Array6m
Construct Suffix Tree from Suffix Array and LCP Array6m
Reading5 readings
Counting Sort10m
Slides and External References2m
Computing the LCP Array - Additional Slides10m
Suffix Tree Construction - Pseudocode10m
Slides and External References2m
Quiz1 practice exercise
Suffix Array Construction12m
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83%

got a tangible career benefit from this course

Top Reviews

By HCMay 7th 2018

Excelentes algoritmos, nunca había pensado lo complicado que era hacer pattern matching eficientemente en términos de tiempo de procesamiento y memoria.

By PGNov 19th 2017

great course, interesting concepts and very well delivered content from lecture videos. challenging and rewarding programming assignments.

Instructors

Alexander S. Kulikov

Visiting Professor
Department of Computer Science and Engineering

Michael Levin

Lecturer
Computer Science

Pavel Pevzner

Professor
Department of Computer Science and Engineering

Neil Rhodes

Adjunct Faculty
Computer Science and Engineering

About University of California San Diego

UC San Diego is an academic powerhouse and economic engine, recognized as one of the top 10 public universities by U.S. News and World Report. Innovation is central to who we are and what we do. Here, students learn that knowledge isn't just acquired in the classroom—life is their laboratory....

About National Research University Higher School of Economics

National Research University - Higher School of Economics (HSE) is one of the top research universities in Russia. Established in 1992 to promote new research and teaching in economics and related disciplines, it now offers programs at all levels of university education across an extraordinary range of fields of study including business, sociology, cultural studies, philosophy, political science, international relations, law, Asian studies, media and communications, IT, mathematics, engineering, and more. Learn more on www.hse.ru...

About the Data Structures and Algorithms Specialization

This specialization is a mix of theory and practice: you will learn algorithmic techniques for solving various computational problems and will implement about 100 algorithmic coding problems in a programming language of your choice. No other online course in Algorithms even comes close to offering you a wealth of programming challenges that you may face at your next job interview. To prepare you, we invested over 3000 hours into designing our challenges as an alternative to multiple choice questions that you usually find in MOOCs. Sorry, we do not believe in multiple choice questions when it comes to learning algorithms...or anything else in computer science! For each algorithm you develop and implement, we designed multiple tests to check its correctness and running time — you will have to debug your programs without even knowing what these tests are! It may sound difficult, but we believe it is the only way to truly understand how the algorithms work and to master the art of programming. The specialization contains two real-world projects: Big Networks and Genome Assembly. You will analyze both road networks and social networks and will learn how to compute the shortest route between New York and San Francisco (1000 times faster than the standard shortest path algorithms!) Afterwards, you will learn how to assemble genomes from millions of short fragments of DNA and how assembly algorithms fuel recent developments in personalized medicine....
Data Structures and Algorithms

Frequently Asked Questions

  • Once you enroll for a Certificate, you’ll have access to all videos, quizzes, and programming assignments (if applicable). Peer review assignments can only be submitted and reviewed once your session has begun. If you choose to explore the course without purchasing, you may not be able to access certain assignments.

  • When you enroll in the course, you get access to all of the courses in the Specialization, and you earn a certificate when you complete the work. Your electronic Certificate will be added to your Accomplishments page - from there, you can print your Certificate or add it to your LinkedIn profile. If you only want to read and view the course content, you can audit the course for free.

More questions? Visit the Learner Help Center.