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
Genome revolutionhttps://www.youtube.com/watch?v=u8bsCiq6hvM
DETOUR: array design
Affymetrix GeneChip® microarray design
http://www.oceanridgebio.com/affymetrix-gene-chip.html
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
Oxford Nanopore MinION
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
Human full genome: 3234,8 Mb
Tallinn - Jõgeva - Misso: 320 km
ATGCTCGTAC = 1mm
NGS strategies
http://www.nature.com/nrd/journal/v12/n5/full/nrd3979.html
Genomic data
http://www.ncbi.nlm.nih.gov/genbank/statistics
Growth of GenBank and WGS
Databases
https://www.ncbi.nlm.nih.gov/sra
http://www.ebi.ac.uk/ena
Chapter 3 videos
https://www.youtube.com/playlist?list=PLQ-85lQlPqFNGdaeGpV8dPEeSm3AChb6L
http://bioinformaticsalgorithms.com/index.htm
Recap video lectures
Newspaper experiment
k-mer composition of a sequence
ATGCATACTGTTATGGAGC k = 3
Recap video lectures
Hamiltonian path finding problem
vs
de Bruijn graphATGCATACTGTTATGGAGC k = 3
Recap video lectures
Eulerian path finding problem (Eulerian theorem)
Universal string problemk = {2,3}
Recap video lectures
Hamilton vs Euler
Paired de Bruijn graph
ATGCATACTGTTATGGAGC k = 3, d = 1
PROBLEMS WITH REALITY
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
Chapter 3 homeworkhttp://rosalind.info/classes/337/
Due 19.10.16 midnight
tasks 23-35: choose min 6, max 9 tasks
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