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Bioinformatics 2021

Genomics and DNA analysis

23 September 2021

Things to do

This course teach how to interpret and understand the results of bioinformatic analyses. Most molecular biologists will work in team with (or hire) bioinformatic teams, so even if they do not use the tools, all molecular biologists need to understand what is the meaning of the results. It is important to speak the same language, and be aware of the key aspects that can lead to the experiment’s success or failure.

Classes

Here you will find the slides from the classes and other supplementary material. Notice that some things are said but not written, so you better take good notes. We recommend taking notes with pen and paper using the Cornell Method.

Sequences used in classes

Attendance

By regulation from the Rectory, students need to attend at least 70% of the classes. If you cannot attend, you must deliver all homework on time. Late submissions will not be accepted.

The attendance book is updated every week and can be seen in Google Sheets.

Prerequisites

This course does not require knowledge of coding or programming, but it will always be a strong advantage —in this course and in professional life— to know how to code a program.

You will need:

We recommend (but not require):

Syllabus

We follow partially the plan proposed by Sayres (2018)Sayres, et al. “Bioinformatics Core Competencies for Undergraduate Life Sciences Education.” PLoS ONE 13, no. 6 (2018): 1–20. https://doi.org/10.1371/journal.pone.0196878.

. At the end of the course students should be able to:

Online supplementary material

Bibliography

The list of recommended and mandatory papers is in a separate page.

Web references

NCBI Videos: Sequences

These videos are complementary to our classes. They cover the same topics with more detail. Please watch them to understand better this course. + NCBI Minute: A Beginner’s Guide to Genes and Sequences at NCBI (33:44) + NCBI Minute: How to Quickly Retrieve Sequences from NCBI (23:38) + NCBI: Download a custom set of records (03:11) + NCBI: Retrieve Sequences for an Organism (01:36) + Obtain Genomic Sequence for a gene (02:47) + Webinar: Accessing 1000 Genomes Data at NCBI (32:15) + NCBI Minute: Important Changes Coming to the Sequence Databases - GI Numbers (24:26)

NCBI Genome Visualization

Searching

BLAST

General Literature

Originally published at https://anaraven.bitbucket.io/blog/2021/bioinfo/