460-6025/02 – Algorithms for Bioinformatics (ABI)
| Gurantor department | Department of Computer Science | Credits | 10 |
| Subject guarantor | prof. RNDr. Václav Snášel, CSc. | Subject version guarantor | prof. RNDr. Václav Snášel, CSc. |
| Study level | postgraduate | Requirement | Choice-compulsory type B |
| Year | | Semester | winter + summer |
| | Study language | English |
| Year of introduction | 2019/2020 | Year of cancellation | |
| Intended for the faculties | FEI | Intended for study types | Doctoral |
Subject aims expressed by acquired skills and competences
The aim of the course is to provide students deeper overview of design and implementation of algorithms and data structures. In addition, this knowledge and skills will be further enhanced in a direction that is in line with the specific focus of its Ph.D. studies and dissertation work.
Teaching methods
Seminars
Individual consultations
Project work
Other activities
Summary
The course is focused on biological applications, computational problems, and their various advanced algorithmic solutions. Students will be introduced, in-depth, to the algorithmic techniques applied in bioinformatics. Each topic provides the biological motivation and precisely defines the corresponding computational problems; different methods and the corresponding algorithms are also presented including detailed examples to illustrate each algorithm.
Compulsory literature:
• Sung, W. K. (2009). Algorithms in bioinformatics: A practical introduction. CRC Press.
• Compeau, Phillip, and Pavel Pevzner. Bioinformatics algorithms: an active learning approach. Vol. 1. La Jolla: Active Learning Publishers, 2015.
• Zvelebil, Marketa J., and Jeremy O. Baum. Understanding bioinformatics. Garland Science, 2007.
Recommended literature:
• M. Dorigo, T. Stützle, Ant Colony Optimization, MIT Press, Cambridge, MA, 2004.
• A. Engelbrecht, Computational Intelligence: An Introduction, 2nd Edition, Wiley, New York, NY, USA, 2007.
Additional study materials
Way of continuous check of knowledge in the course of semester
Continuous monitoring of study activities and assigned tasks during regular consultations. If some publication activity will be a part of the student's tasks, the relevant article would be presented in the course.
Oral exam.
E-learning
Other requirements
The student prepares and presents the work on a given topic.
Prerequisities
Subject has no prerequisities.
Co-requisities
Subject has no co-requisities.
Subject syllabus:
• Sequence similarity
• Suffix trees
• Genome alignment and multiple sequence alignment
• Database search
• Phylogeny Reconstruction and Comparison
• Genome Rearrangement
• Motif Finding
• RNA secondary structure prediction
• Peptide Sequencing
• Population genetics
• BAM algorithm for resequencing, BLAST and BLAT algorithms description
• Assembly algoritms, paired-end scaffolding algorithms
Conditions for subject completion
Occurrence in study plans
Occurrence in special blocks
Assessment of instruction
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