Blog of Andrés Aravena
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Bioinformatics

Genomics and DNA analysis

01 September 2018

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 .

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.

[Slides]. + Class 20: Multiple Alignment. (Dec 11, 2018). Aligning more than two sequences at the same time [Slides]. + Class 21: Practice. (Dec 14, 2018).

[Slides]. + Last Steps in SNP finding. (Dec 21, 2018). Some things you need to know. [Slides]. + Class 24: Alignment free methods. (Dec 25, 2018). Finding Motifs and Taxonomy Identification without alignment. [Slides].

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.

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:

web references

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