22,612

#### 100% online

Start instantly and learn at your own schedule.

#### Approx. 17 hours to complete

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

#### English

Subtitles: English

### Skills you will gain

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

#### 100% online

Start instantly and learn at your own schedule.

#### Approx. 17 hours to complete

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

#### English

Subtitles: English

### Syllabus - What you will learn from this course

Week
1
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....
5 videos (Total 27 min), 5 readings, 1 quiz
5 videos
Brute Force Approach to Pattern Matching2m
Herding Patterns into Trie5m
Herding Text into Suffix Trie6m
Suffix Trees4m
Trie Construction - Pseudocode10m
FAQ10m
Slides and External References10m
Available Programming Languages10m
FAQ on Programming Assignments10m
Week
2
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....
5 videos (Total 30 min), 4 readings, 1 quiz
5 videos
Inverting Burrows-Wheeler Transform7m
Using BWT for Pattern Matching6m
Suffix Arrays5m
Approximate Pattern Matching6m
Using BWT for Pattern Matching10m
Pattern Matching with Suffix Array10m
FAQ10m
Slides and External References10m
Week
3
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....
5 videos (Total 35 min), 2 readings, 1 quiz
5 videos
Safe Shift3m
Prefix Function7m
Computing Prefix Function9m
Knuth-Morris-Pratt Algorithm5m
Programming Assignment 3 lasts for two weekss
Slides and External References10m
1 practice exercise
Exact Pattern Matching30m
Week
4
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....
11 videos (Total 76 min), 5 readings, 2 quizzes
11 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
Counting Sort10m
Slides and External References2m
Computing the LCP Array - Additional Slides10m
Suffix Tree Construction - Pseudocode10m
Slides and External References2m
1 practice exercise
Suffix Array Construction12m
4.5
103 Reviews

## 50%

started a new career after completing these courses

## 42%

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

Lecturer
Computer Science

### Pavel Pevzner

Professor
Department of Computer Science and Engineering

### Neil Rhodes

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 communicamathematics, 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....