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Algorithms on Strings

Alexander S. Kulikov, Michael Levin, Pavel Pevzner, and Neil Rhodes

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. In this online course you will learn key pattern matching concepts: tries, suffix trees, suffix arrays and even the Burrows-Wheeler transform.

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What's inside

Syllabus

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.

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Taught by Pavel Pevzner and Neil Rhodes, who are recognized for their work in algorithm design in genomics

Offers hands-on practice through programming assignments

Provides a foundational understanding of key pattern matching concepts used in text search and genomic research

Covers advanced topics such as the Burrows-Wheeler Transform and suffix arrays

May require prerequisites in data structures, algorithms, and potentially biology, depending on the student's background

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Reviews summary

Rigorous foundation in string algorithms

According to learners, this course offers a deep and rigorous dive into essential string algorithms, making it highly valuable for those seeking a strong theoretical foundation. Students note the course covers complex topics like suffix trees and the Burrows-Wheeler Transform. However, many reviewers found the course, particularly the programming assignments, to be very challenging, often requiring a stronger prerequisite background than anticipated. While demanding, successfully completing the assignments is often highlighted as rewarding and effective for solidifying understanding.

Lectures can be dense and fast-paced.

"The lectures are very dense and require multiple rewatches to fully absorb the material."

"Concepts like suffix trees are explained thoroughly but the pace is fast."

"Needed to supplement lectures with external resources to fully grasp some topics."

Programming tasks are rigorous yet valuable.

"The programming assignments, while hard, solidify the concepts taught in lectures."

"Spent days on the suffix array construction problem, it was a significant hurdle."

"Successfully completing the assignments feels very rewarding and reinforces learning."

Provides deep theoretical coverage of algorithms.

"Excellent theoretical depth. Pavel and Michael explain complex ideas well..."

"Covers essential topics like KMP and Burrows-Wheeler Transform, very relevant for bioinformatics."

"This course significantly improved my understanding of string algorithms."

Needs solid data structures/algorithms background.

"Prerequisites are higher than stated. Need a strong background in data structures and algorithms."

"Learners should have a solid computer science foundation before attempting this course."

"Felt lost without a strong grasp of prerequisite material."

Course difficulty level is notably high.

"Assignments are incredibly challenging. Spent days on the suffix array construction."

"One of the most challenging courses I've taken, but also one of the most rewarding..."

"This course is NOT for beginners and requires significant time investment."

"The assignments are unreasonably difficult for the time allotted. Many students seemed to struggle."

Activities

Be better prepared before your course. Deepen your understanding during and after it. Supplement your coursework and achieve mastery of the topics covered in Algorithms on Strings with these activities:

Organize and Review Course Materials

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Organize your lecture notes, assignments, and other course materials to enhance your ability to locate and review important information.

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Gather all relevant course materials
Create an organized system for storage and retrieval

Review Foundations of Data Structures and Algorithms

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Refresh your knowledge of basic data structures and algorithms to ensure a solid foundation for understanding advanced pattern matching techniques.

Browse courses on Data Structures

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Review lecture notes or textbooks
Solve practice problems

Read Algorithms on Strings, Trees, and Sequences

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Review this foundational text on algorithms for strings, trees, and sequences to enhance your understanding of key concepts covered in the course.

View Integer Linear Programming in Computational and... on Amazon

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Read and understand the relevant chapters
Solve exercises and practice problems

Four other activities

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Show all seven activities

Explore Burrows-Wheeler Transform Applications

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Seek out and follow tutorials to gain insights into the practical applications of the Burrows-Wheeler Transform in various fields.

Browse courses on Burrows-Wheeler Transform

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Identify relevant tutorials
Watch and follow the tutorials
Apply the learned concepts to practice examples

Discuss Implementation Strategies for Suffix Arrays

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Engage with peers to exchange ideas and strategies for implementing suffix arrays, deepening your understanding and broadening your knowledge.

Browse courses on Suffix Arrays

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Form a study group with peers
Research and gather different implementation approaches
Share and discuss your findings

Visualize Suffix Trees

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Create a visual representation of suffix trees to enhance your comprehension and strengthen your mental model of their structure and functionality.

Browse courses on Suffix Trees

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Choose a visualization tool or technique
Gather data on suffix tree structures
Design and create your visualization

Knuth-Morris-Pratt Algorithm Practice

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Practice using the Knuth-Morris-Pratt Algorithm for exact pattern matching to solidify your understanding and improve your proficiency.

Browse courses on Knuth-Morris-Pratt Algorithm

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Review the Knuth-Morris-Pratt Algorithm
Implement the algorithm in your preferred programming language
Solve practice problems and test cases

Career center

Learners who complete Algorithms on Strings will develop knowledge and skills that may be useful to these careers:

Biostatistician

A Biostatistician designs and analyzes experiments, collects and analyzes data, and interprets the results to answer biological or medical questions. A course in Algorithms on Strings will provide you with the skills necessary to perform data analysis and interpretation. The course covers topics such as suffix trees, suffix arrays, and the Burrows-Wheeler transform, which are all important topics in bioinformatics. This course will help you build a foundation for a career in biostatistics.

See salaries and explore the career path for Biostatistician

Bioinformatician

A Bioinformatics develops and applies computational tools and techniques to analyze biological data. A course in Algorithms on Strings will provide you with the skills necessary to develop and apply these tools. The course covers topics such as suffix trees, suffix arrays, and the Burrows-Wheeler transform, which are all important topics in bioinformatics. This course will help you build a foundation for a career in bioinformatics.

See salaries and explore the career path for Bioinformatician

Computational Biologist

A Computational Biologist develops and applies computational tools and techniques to analyze biological data. A course in Algorithms on Strings will provide you with the skills necessary to develop and apply these tools. The course covers topics such as suffix trees, suffix arrays, and the Burrows-Wheeler transform, which are all important topics in bioinformatics. This course will help you build a foundation for a career in computational biology.

See salaries and explore the career path for Computational Biologist

Statistician

A Statistician collects, analyzes, and interprets data to answer questions. A course in Algorithms on Strings will provide you with the skills necessary to analyze and interpret data. The course covers topics such as suffix trees, suffix arrays, and the Burrows-Wheeler transform, which are all important topics in statistics. This course will help you build a foundation for a career in statistics.

See salaries and explore the career path for Statistician

Data Scientist

A Data Scientist collects, analyzes, and interprets data to answer business questions. A course in Algorithms on Strings will provide you with the skills necessary to analyze and interpret data. The course covers topics such as suffix trees, suffix arrays, and the Burrows-Wheeler transform, which are all important topics in data science. This course will help you build a foundation for a career in data science.

See salaries and explore the career path for Data Scientist

Database Administrator

A Database Administrator designs, implements, and maintains databases. A course in Algorithms on Strings will provide you with the skills necessary to design, implement, and maintain databases. The course covers topics such as suffix trees, suffix arrays, and the Burrows-Wheeler transform, which are all important topics in database management. This course will help you build a foundation for a career in database administration.

See salaries and explore the career path for Database Administrator

Security Analyst

A Security Analyst identifies and protects computer systems and data from unauthorized access, use, disclosure, disruption, modification, or destruction. A course in Algorithms on Strings will provide you with the skills necessary to protect computer systems and data. The course covers topics such as suffix trees, suffix arrays, and the Burrows-Wheeler transform, which are all important topics in security analysis. This course will help you build a foundation for a career in security analysis.

See salaries and explore the career path for Security Analyst

Information Security Analyst

An Information Security Analyst protects computer systems and data from unauthorized access, use, disclosure, disruption, modification, or destruction. A course in Algorithms on Strings will provide you with the skills necessary to protect data from unauthorized access. The course covers topics such as suffix trees, suffix arrays, and the Burrows-Wheeler transform, which are all important topics in information security. This course will help you build a foundation for a career in information security.

See salaries and explore the career path for Information Security Analyst

Machine Learning Engineer

A Machine Learning Engineer develops and deploys machine learning models to solve business problems. A course in Algorithms on Strings will provide you with the skills necessary to develop and deploy machine learning models. The course covers topics such as suffix trees, suffix arrays, and the Burrows-Wheeler transform, which are all important topics in machine learning. This course will help you build a foundation for a career in machine learning engineering.

See salaries and explore the career path for Machine Learning Engineer

Software Engineer

A Software Engineer designs, develops, and maintains software systems. A course in Algorithms on Strings will provide you with the skills necessary to design, develop, and maintain software systems. The course covers topics such as suffix trees, suffix arrays, and the Burrows-Wheeler transform, which are all important topics in software engineering. This course will help you build a foundation for a career in software engineering.

See salaries and explore the career path for Software Engineer

Systems Analyst

A Systems Analyst studies how a business works to identify opportunities for improvement. A course in Algorithms on Strings will provide you with the skills necessary to analyze business processes and identify opportunities for improvement. The course covers topics such as suffix trees, suffix arrays, and the Burrows-Wheeler transform, which are all important topics in systems analysis. This course will help you build a foundation for a career in systems analysis.

See salaries and explore the career path for Systems Analyst

Network Analyst

A Network Analyst designs, implements, and maintains computer networks. A course in Algorithms on Strings will provide you with the skills necessary to design, implement, and maintain computer networks. The course covering topics such as suffix trees, suffix arrays, and the Burrows-Wheeler transform, which are all important topics in network analysis. This course will help you build a foundation for a career in network analysis.

See salaries and explore the career path for Network Analyst

Quality Assurance Analyst

A Quality Assurance Analyst tests software to ensure that it meets the requirements of the user. A course in Algorithms on Strings will provide you with the skills necessary to test software. The course covers topics such as suffix trees, suffix arrays, and the Burrows-Wheeler transform, which are all important topics in software testing. This course will help you build a foundation for a career in quality assurance.

See salaries and explore the career path for Quality Assurance Analyst

Information Architect

An Information Architect designs and develops the structure and organization of websites. A course in Algorithms on Strings will provide you with the skills necessary to design and develop the structure and organization of websites. The course covers topics such as suffix trees, suffix arrays, and the Burrows-Wheeler transform, which are all important topics in information architecture. This course will help you build a foundation for a career in information architecture.

See salaries and explore the career path for Information Architect

Web Developer

A Web Developer designs and develops websites. A course in Algorithms on Strings will provide you with the skills necessary to design and develop websites. The course covers topics such as suffix trees, suffix arrays, and the Burrows-Wheeler transform, which are all important topics in web development. This course will help you build a foundation for a career in web development.

See salaries and explore the career path for Web Developer

Reading list

We've selected 12 books that we think will supplement your learning. Use these to develop background knowledge, enrich your coursework, and gain a deeper understanding of the topics covered in Algorithms on Strings.

Bioinformatics Algorithms

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Covers many of the key topics in the course, including suffix trees, the Burrows-Wheeler transform, and approximate pattern matching. It can be seen as a more in-depth theoretical treatment of many of the concepts covered in the course.

Algorithms on Strings

Two deals to help you save

What's inside

Syllabus

Traffic lights

Save this course

Reviews summary

Rigorous foundation in string algorithms

Activities

Career center

Reading list

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