Algorithms in Bioinformatics


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BIOINF4361 - Advanced Sequence Analysis

Title
BIOINF4361 - Advanced Sequence Analysis
Lecturer Monika Balvočiūtė (Visiting lecturer, Teach@Tuebingen program), Mohamed El Hadidi and Prof. Daniel Huson
Venue Thursdays, 8:15-10:00, Großer Hörsaal, Sand 6/7
Problem sessions
Tuesdays, 10-12h, Großer Hörsaal, Sand 6/7 (starting 27.10.2015)
Modules MSc Bioinformatik: Wahlpflichtmodul Bioinformatik und Wahlpflichtmodul Informatik
MSc Informatik: Wahlpflichtmodul Informatik
See http://campus.verwaltung.uni-tuebingen.de/20152d126091
Grading Final exam (100%) + assignments (extra points)
Language English

 

Contents

This lecture will look at advanced topics in sequence analysis.

Weekly assignments are handed out in class.

The course is based on a book by Mäkinen et al and journal articles, which will be handed out during the course.
 

 

Date Topic Assignments
14/10/15 
1. Introduction
Sequencing videos
Introduction to Next-Generation Sequencing
Comparison of Next-Generation Sequencing Systems
Textbook
Assignment 1
example file 1
example file 2
example file 3
22/10/15 2. Suffix arrays (Chapter 8 Classical indexes) Assignment 2
29/10/15 continued (Space efficient linear time construction of suffix arrays)
3. Suffix trees (Chapter 8)
Assignment 3
05/11/15 4. Burrows-Wheeler indexes (Chapters 9 and 3) Assignment 4
12/11/15 continued
Complexity graph
Assignment 5
19/11/15 continued (Bidirectional BWI and suffix trees) Assignment 6
26/11/15 5. Alignment-free genome comparisons (Chapter 11) Assignment 7
03/12/15 continued  Assignment 8
ST
10/12/15 6. Taxonomic diversity
Human Microbiome Analysis
Assignment 9
Fasta File
Metadata
17/12/15 7. Genome compression (Chapter 12)
Trends in Genome Compression
Assignment 10
7/01/16
8. Fragment assembly (Chapter 13)
14/01/16 9. Variation calling and haplotype phasing (Chapter 14)
A framework for variation discovery and genotyping...
WhatsHap: Weighted Haplotype Assembly...
Assignment 11
21/01/16 10. Motif finding
Unsupervised Learning of Multiple Motifs in Biopolymers...
An algorithm for finding signals of unknown length...
Assignment 12
28/01/16 Slides

4/02/16 Sequence analysis projects
Projects slides
Practice exam
11/02/16 10am Final exam

 

Literature

Mäkinen et al, Genome-scale Algorithm Design, 2015

 

How to get credit for this course

  • Always participate in the weekly problem sessions and actively present your results. Obtain at least 50% of all points.
  • Pass the final exam
  • You may work on and hand-in assignments in groups of up to two people.
  • Assignments are set every Thursday and are due on at the beginning of the lecture on the following Thursday.
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