4. Assessment 2: Calling Real Genes¶

4.1. Running the Tool¶

1. Launch Firefox or Chrome, and browse to https://cpt.tamu.edu/galaxy/.
2. Once Galaxy has loaded, you will need to run this tool.
3. Click execute.
4. Like the assessment last week, the tool will output a single dataset. Click the eyeball icon to access the assessment organism in Apollo.

4.2. Annotation in Apollo¶

You will be annotating genes in Apollo. To do this you will need to look at each coding sequence and identify the ones which are likely genes, and ignore the rest.

First, turn on a few tracks in Apollo. We recommend first turning on MetaGeneAnnotator and Glimmer3 before turning on Sixpack. This reflects the order you will want to consider evidence in: most trustworthy evidence (i.e. real gene callers) before the less trustworthy evidence (i.e. sixpack which simply lists all possible coding sequence regions.)

Look through the DNA and make what you believe to be the most accurate, educated guess of where genes are in the genome. Consider the things you have learnt in lecture about how phages behave and which gene calls they might prefer. For each possible gene call consider the evidence before right-clicking the evidence, selecting “Create a Feature” and selecting “gene”. You do not need to rename your features during this exercise.

Sometime soon we will talk about common mistakes we saw. This way everyone can learn from the possible gene call issues, and everyone can make optimal gene calls.