using graphs to assemble genomes - ut · bioinformatics course (13.10, here) models and methods for...

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

http://www.ebi.ac.uk/~nf/hts_mappers/

Sequence alignment

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