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September 26, 2023

GENOME VISUALIZATION

Learning Checklist:
1. Know how to use Artemis to find annotated features in genomic sequences
2. Know how to create genomic maps using DNAPlotter
3. Know how to leverage Unix commands to create spreadsheet-compatible files from text files.

E. Genome visualization
Artemis is one of many genome browsers that make it possible to view and edit the features found in genomes. In these tutorials, we will learn how to get around a genome in Artemis, to find features such as protein coding sequences, repetitive sequences or transposons, and to generate graphs that provide insights into regions of the genome. We will also learn how to generate publication-quality custom plots of genomes. As well, we will give a brief example of how Unix commands can be used to create data pipelines that process human-readable text files produced by Artemis into a form that is machine-readable.

Although we will not cover this topic, Artemis is also equipped for the purposes of de-novo annotation of a newly-sequenced genome, and for editing existing genome annotations.
1. Artemis basics  - we will do only Exercises 1 and 2 from this tutorial.
2. DNAPlotter
3. Artemis - extracting features from text files
 
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Lecture 3, part 2 of 2
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