Please note that the text below is not final.
Material made available in Canvas
- lecture presentations
- articles
- exercises and their solutions
- self-study questions
Books
You may use either the new one-volume third edition (2018) of the book (recommended) or the two-volume set of the second edition (2015).
Third edition (1 volume):
- Philip Compeau & Pavel Pevzner (2018) Bioinformatics Algorithms: An Active Learning Approach, 3rd Edition. Active Learning Publishers. ISBN 9780990374633.
Second edition (2 volumes):
- Philip Compeau & Pavel Pevzner (2015) Bioinformatics Algorithms: An Active Learning Approach, 2nd Edition, Vol. I. Active Learning Publishers. ISBN 9780990374619.
- Philip Compeau & Pavel Pevzner (2015) Bioinformatics Algorithms: An Active Learning Approach, 2nd Edition, Vol. II. Active Learning Publishers. ISBN 9780990374626.
There is also a first edition of the book from 2014, but it does not cover all the topics of the course, so it is not recommended.
There is a website for the book with additional material and information, including videos with lectures covering many of the subjects.
All of the book actually now seems to be available online. Please see the links below for each chapter.
Akademika is unfortunately unable to get hold of the book. It seems to be available only from the publisher or from amazon.com.
Detailed list of book sections included in syllabus
Below is a detailed list of sections of the books that are included in the syllabus. Page numbers are first indicated for the second edition and then for the third edition [in square brackets]:
Volume I
Chapter 1 (Intro)
Only the following sections are part of the syllabus:
- Big-O notation (page 52 [53])
- Directionality of DNA strands (page 59 [60])
Chapter 2 (Motif discovery)
The entire chapter is part of the syllabus, except:
- Epilogue (pages 104-106 [105-107])
- Charging station (pages 107 [108])
- Detour: Buffon’s needle (109-112 [110-113])
Chapter 3 (Genome Assembly)
The entire chapter is part of the syllabus, except:
- Detours (some) (pages 172-179 [174-182])
Chapter 4 (Brute force algorithms)
This chapter is not part of the syllabus.
Chapter 5 (Dynamic programming)
The entire chapter is part of the syllabus, except:
- Detours (some) (pages 282-284 [286-288])
Chapter 6 (Combinatorial problems)
Only the following sections are part of the syllabus:
- Genomic dot-plots (page 325-328 [330-333])
Volume II
Chapter 7 (Phylogeny)
The entire chapter is part of the syllabus, except:
- Detours (all) (pages 51-65 [401-414])
Chapter 8 (Clustering)
The entire chapter is part of the syllabus, except:
- Detours (some) (pages 111, 113-117 [461-466])
Chapter 9 (Mapping and searching)
The entire chapter is part of the syllabus, except:
- Detours (some) (pages 170-176 [521-527])
Chapter 10 (Hidden Markov Models)
The first part of the chapter is part of the syllabus (pages 178-217 [530-569])
Chapter 11 (Proteomics)
Only the following sections are part of the syllabus:
- Gene prediction (page 273-274 [626-627])
In 2020, gene prediction and chapter 11 is NOT part of the syllabus.