This is the English language version of the Bioinformatics course. The main subject is “metagenomics”. We will learn how to handle the output of DNA sequencing machines, how to assemble the chromosome, how to find genes and how to determine the probable function of the proteins they encode. If time allows, we will also study phylogenetic trees and microarray analysis.
Classes are held each week on Tuesdays at 13:00 (at the Astronomy Dept. Computer Lab) for 120 minutes, and on Fridays at 13:30 (at Physics Dept. Computer Lab). for about 80 minutes. Most of the practice is done on Linux servers, so you may be interested in other courses with that subject.
Please register yourself in the course forum at https://groups.google.com/d/forum/iu-bioinfo. You can also participate writing an email to iu-bioinfo@googlegroups.com.
This page will be updated during the semester. Please check it regularly.
Classes
Here you find the slides that have been used in classes. Notice that usually they are not published immediately, so you better take good notes. We recommend taking notes with pen and paper using the Cornell Method.
Class 1: Why do we care about Bioinformatics?. (Sep 18, 2018). [Slides].
A personal perspective on Metagenomics and BioinformaticsClass 2: Introductory Workshop. (Sep 21, 2018). [Document].
Based on the extension activities of project Nucleo Milenio P01-005 “Information and Randomness” at Universidad de Chile. Original date October 14, 2005Class 3: DNA sequencing and assembly. (Sep 25, 2018). [Document].
How can we know the DNA sequence? (Incomplete)Class 4: Assembly statistics. (Sep 28, 2018). [Slides].
Which technology is better for your budget?Class 5: Designing a Sequencing Project. (Oct 2, 2018). [Slides].
Depth, Coverage breadth, Number of Contigs, N50. Lander-Waterman theory applied to Overlay-Layout-Consensus assemblyClass 6: DNA Sequencing Technologies Overview. (Oct 5, 2018). [Document].
Presentations of homework by studentsClass 7: Aligning reads to a reference. (Oct 12, 2018). [Slides].
Also, how to get public sequence dataClass 8: Aligning reads to a reference. (Oct 16, 2018). [Slides].
Also, Summary of NGS alternatives (homework answers)Class 9: BWA. (Oct 19, 2018). [Slides].
Also, Summary of homework AnswersClass 10: SAM, BAM & BWA. (Oct 23, 2018). [Slides].
Also, Summary of homework AnswersClass 11: Summary for Midterms. (Oct 23, 2018). [Slides].
Class 12: Alignment. (Nov 13, 2018). [Slides].
Counting differences between sequences. Hamming and Edit (Levenshtein) distancesClass 13: Global and Semi-global Alignments. (Nov 16, 2018). [Slides].
Needleman-Wunsch method for finding maximal alignment score. Discussion of match, mismatch and gap scoresClass 14: Local Alignments. (Nov 20, 2018). [Slides].
Smith-Waterman method for finding optimal local alignment score, and traceback to find the actual alignment(s)Class 15: Understanding BLAST. (Nov 23, 2018). [Slides].
Using NCBI websiteClass 16: Scores and probabilities. (Nov 27, 2018). [Slides].
StatisticsClass 17: NCBI Entrez. (Nov 30, 2018). [Slides].
Using NCBI websiteClass 18: E-value. (Dec 4, 2018). [Slides].
StatisticsClass 19: Homework Answers & Exam question. (Dec 6, 2018). [Slides].
Class 20: Multiple Alignment. (Dec 11, 2018). [Slides].
Aligning more than two sequences at the same timeClass 21: Practice. (Dec 14, 2018). [Slides].
Last Steps in SNP finding. (Dec 21, 2018). [Slides].
Some things you need to know.Class 24: Alignment free methods. (Dec 25, 2018). [Slides].
Finding Motifs and Taxonomy Identification without alignment.
Homework
All homework should be sent to andres.aravena+bioinfo@istanbul.edu.tr before the deadline to get a grade. Please make sure that you send your work to the correct address, otherwise you will get a grade zero.
Homework: Genome assemblers (Deadline: Friday 22 January at 9:00).
Homework 2 – DNA assemblers (Deadline: Tuesday 16 October at 13:00).
Homework 1 – Next Generation Sequences (Deadline: Friday 12 October at 13:30).
Semester Project
The challenge is to sequence your own samples. For this, during the semester, you have to work as a team and follow these steps:
- Learn what technologies exist for DNA sequencing
- Learn which companies provide sequencing services, in the country and abroad
- Learn the prices of the service
- Decide the target to sequence and the scientific question to answer
- Decide the sampling and DNA extraction protocols
- Decide how to get money to cover the expenses
- Perform the sampling and DNA extraction
- Send the DNA and receive the sequences
- Analyze and conclude
- Deposit the sequences in an international database
web references
- ftp://ftp.ncbi.nlm.nih.gov/pub/factsheets
- BLAST topics
- BLAST documentation
- Entrez Help
- NCBI YouTube Channel
Attendance
By regulation from the Rectory, students need to attend at least 70% of the classes. The attendance book is updated every week and can be seen in Google Sheets.
Bibliography
Chou, H.-H., and M. H. Holmes. “DNA Sequence Quality Trimming and Vector Removal.” Bioinformatics 17, no. 12 (2001): 1093–1104. doi:10.1093/bioinformatics/17.12.1093.
Sims, David, Ian Sudbery, Nicholas E. Ilott, Andreas Heger, and Chris P. Ponting. “Sequencing Depth and Coverage: Key Considerations in Genomic Analyses.” Nature Reviews Genetics 15, no. 2 (2014): 121–32. doi:10.1038/nrg3642.
Li, Zhenyu, Yanxiang Chen, Desheng Mu, Jianying Yuan, Yujian Shi, Hao Zhang, Jun Gan, et al. “Comparison of the Two Major Classes of Assembly Algorithms: Overlap-Layout-Consensus and de-Bruijn-Graph.” Briefings in Functional Genomics 11, no. 1 (2012): 25–37. doi:10.1093/bfgp/elr035.
Nagarajan, Niranjan, and Mihai Pop. “Sequence Assembly Demystified.” Nature Reviews. Genetics 14, no. 3 (2013): 157–67. doi:10.1038/nrg3367.
Dina Fine Maron. “Dirty Money.” Scientific American, 2017. https://www.scientificamerican.com/article/dirty-money/.
Jeff Leach. “Going Feral: My One-Year Journey to Acquire the Healthiest Gut Microbiome in the World,” January 2014. http://humanfoodproject.com/going-feral-one-year-journey-acquire-healthiest-gut-microbiome-world-heard/.
Phillippy, Adam M. “New Advances in Sequence Assembly.” Genome Research 27, no. 5 (May 1, 2017): xi–xiii. doi:10.1101/gr.223057.117.
Tyson, Gene W, Jarrod Chapman, Philip Hugenholtz, Eric E Allen, Rachna J Ram, Paul M Richardson, Victor V Solovyev, Edward M Rubin, Daniel S Rokhsar, and Jillian F Banfield. “Community Structure and Metabolism through Reconstruction of Microbial Genomes from the Environment.” Nature 428, no. 6978 (2004): 37–43. doi:10.1038/nature02340.
Qin, Junjie, Ruiqiang Li, Jeroen Raes, Manimozhiyan Arumugam, Kristoffer Solvsten Burgdorf, Chaysavanh Manichanh, Trine Nielsen, et al. “A Human Gut Microbial Gene Catalogue Established by Metagenomic Sequencing.” Nature 464, no. 7285 (March 4, 2010): 59–65. doi:10.1038/nature08821.
Ünal, Burcu. “Phylogenetic Analysis of Bacterial Communities in Kefir by Metagenomics.” Izmir Institute of Technology, Turkey, 2008.
Ünal, Burcu Ünsal, and Alper Arslanoğlu. “Phylogenetic Identification of Bacteria within Kefir by Both Culture-Dependent and Culture-Independent Methods.” African Journal of Microbiology Research 7, no. 36 (2013): 4533–38. doi:10.5897/AJMR2013.6064.
Handelsman, Jo. “Metagenomics: Application of Genomics to Uncultured Microorganisms.” Microbiology and Molecular Biology Reviews 68, no. 4 (2004): 669–85. doi:10.1128/MMBR.68.4.669-685.2004.
Baker, Brett J., and Jillian F. Banfield. “Microbial Communities in Acid Mine Drainage.” FEMS Microbiology Ecology 44, no. 2 (2003): 139–52. doi:10.1016/S0168-6496(03)00028-X.
Wooley, John C., and Yuzhen Ye. “Metagenomics: Facts and Artifacts, and Computational Challenges.” Journal of Computer Science and Technology 25, no. 1 (2009): 71–81. doi:10.1007/s11390-010-9306-4.
Sharpton, Thomas J. “An Introduction to the Analysis of Shotgun Metagenomic Data.” Frontiers in Plant Science 5 (June 16, 2014): 209. doi:10.3389/fpls.2014.00209.
Hunter, Chris I, Alex Mitchell, Philip Jones, Craig McAnulla, Sebastien Pesseat, Maxim Scheremetjew, and Sarah Hunter. “Metagenomic Analysis: The Challenge of the Data Bonanza.” Briefings in Bioinformatics 13, no. 6 (November 1, 2012): 743–46. doi:10.1093/bib/bbs020.
Teeling, Hanno, and Frank Oliver Glöckner. “Current Opportunities and Challenges in Microbial Metagenome Analysis–a Bioinformatic Perspective.” Briefings in Bioinformatics 13, no. 6 (December 1, 2012): 728–42. doi:10.1093/bib/bbs039.
Mande, Sharmila S, Monzoorul Haque Mohammed, and Tarini Shankar Ghosh. “Classification of Metagenomic Sequences: Methods and Challenges.” Briefings in Bioinformatics 13, no. 6 (November 1, 2012): 669–81. doi:10.1093/bib/bbs054.