using graphs to assemble genomes - ut · bioinformatics course (13.10, here) models and methods for...
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Using graphs to assemble genomes
Bioinformatics course (MTAT.03.239) 06.10.16 Priit Adler
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Genome revolutionhttps://www.youtube.com/watch?v=u8bsCiq6hvM
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DETOUR: array design
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Affymetrix GeneChip® microarray design
http://www.oceanridgebio.com/affymetrix-gene-chip.html
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Sequencing
Pyrosequencing: https://www.youtube.com/watch?v=nFfgWGFe0aA
Sequencing by synthesis: https://www.youtube.com/watch?v=womKfikWlxM
Overview of 4 types of sequencing: https://www.youtube.com/watch?v=jFCD8Q6qSTM
https://en.wikipedia.org/wiki/DNA_sequencing
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Oxford Nanopore MinION
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For background
• How to sequence genome: https://www.youtube.com/watch?v=N4i6lYfYQzY
• DNA sequencing tech used in Human Genome Project: http://www.nature.com/scitable/topicpage/dna-sequencing-technologies-key-to-the-human-828
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Human full genome: 3234,8 Mb
Tallinn - Jõgeva - Misso: 320 km
ATGCTCGTAC = 1mm
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NGS strategies
http://www.nature.com/nrd/journal/v12/n5/full/nrd3979.html
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Genomic data
http://www.ncbi.nlm.nih.gov/genbank/statistics
Growth of GenBank and WGS
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Databases
https://www.ncbi.nlm.nih.gov/sra
http://www.ebi.ac.uk/ena
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Chapter 3 videos
https://www.youtube.com/playlist?list=PLQ-85lQlPqFNGdaeGpV8dPEeSm3AChb6L
http://bioinformaticsalgorithms.com/index.htm
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Recap video lectures
Newspaper experiment
k-mer composition of a sequence
ATGCATACTGTTATGGAGC k = 3
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Recap video lectures
Hamiltonian path finding problem
vs
de Bruijn graphATGCATACTGTTATGGAGC k = 3
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Recap video lectures
Eulerian path finding problem (Eulerian theorem)
Universal string problemk = {2,3}
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Recap video lectures
Hamilton vs Euler
Paired de Bruijn graph
ATGCATACTGTTATGGAGC k = 3, d = 1
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PROBLEMS WITH REALITY
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Bioinformatics Algorithms
An Active Learning Approach
1st Edition:
www.ester.ee/record=b4422219
2nd Edition:
www.ester.ee/record=b4517979
https://youtu.be/yfXeKPt0nw4
http://bioinformaticsalgorithms.com/index.htm
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Chapter 3 homeworkhttp://rosalind.info/classes/337/
Due 19.10.16 midnight
tasks 23-35: choose min 6, max 9 tasks
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Next weekBioinformatics course (13.10, here)
Models and methods for genotype to phenotype
by Leopold Parts
Bioinformatics seminar (14.10, room from Sulev next week)
Bioinformatics methods for analysing genetic screens and cellular phenotypes
by Leopold Parts