String Processing and Pattern Matching Algorithms
About this courseSkip About this course
The world and internet are full of textual information. We search for information using textual queries and read websites, books and e-mails.
These are all strings from a computer science point of view. To make sense of all this 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.
In this course, part of the Algorithms and Data Structures MicroMasters program, you will learn about:
- suffix trees;
- suffix arrays;
- how other brilliant algorithmic ideas help doctors to find differences between genomes;
- power lightning-fast Internet searches.
At a glance
- Language: English
- Video Transcript: English
- Associated programs:
- MicroMasters® Program in Algorithms and Data Structures
- Associated skills: Data Structures, Search Algorithms, Pattern Matching, Algorithms, Computer Science, Personalized Medicine
What you'll learnSkip What you'll learn
- Key ideas for pattern matching and suffix trees
- Suffix arrays
- Burrows-Wheeler Transform for compression
- Applications of string algorithms in bioinformatics
Weeks 1 and 2: 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.
Week 3 and 4: 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.
Learner testimonialsSkip Learner testimonials
“This class makes string algorithms a very interesting and enjoyable topic. I would highly suggest taking this course. All the material is very well explained so you can really understand why it works and not only how! The programming assignments give you a hands-on experience implementing the different algorithm.”
-- Previous Student