You will find the official syllabus/reading list for IN4030 in Leganto. Below are some details about the book, which parts are included, etc.
Please also see the list of relevant textbook sections and articles for each course week.
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.
Chapters 1-5 of the book are actually freely available online. Please see the links below for each chapter.
It is available directly from the publisher, from Amazon.com and elsewhere. Akademika has previously had problems obtaining the book.
There are a few copies of the second edition available from nearby libraries.
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 indicated for the third edition [and for the second edition in square brackets]:
Volume I
Chapter 1 (Intro)
Only the following sections are part of the syllabus:
- Big-O notation (page 53 [52])
- Directionality of DNA strands (page 60 [59])
Chapter 2 (Motif discovery)
The entire chapter is part of the syllabus, except:
- Epilogue (pages 105-107 [104-106])
- Charging station (pages 108 [107])
- Detour: Buffon’s needle (110-113 [109-112])
Chapter 3 (Genome Assembly)
The entire chapter is part of the syllabus, except:
- Detours (some) (pages 174-182 [172-179])
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 286-288 [282-284])
Chapter 6 (Combinatorial problems)
Only the following section is part of the syllabus:
- Genomic dot-plots (page 330-333 [325-328])
Volume II
Chapter 7 (Phylogeny)
The entire chapter is part of the syllabus, except:
- Detours (all) (pages 401-414 [51-65])
Chapter 8 (Clustering)
The entire chapter is part of the syllabus, except:
- Detours (some) (pages 463-466 [111,113-117])
Chapter 9 (Mapping and searching)
The entire chapter is part of the syllabus.
Chapter 10 (Hidden Markov Models)
The first part of the chapter is part of the syllabus (pages 530-569 [178-217])
Chapter 11 (Proteomics)
Only the following section is part of the syllabus:
Gene prediction (page 626-627 [273-274])