Exercise II Group Presentation

Group work on the analysis.

1. Apply EasyGene (Links to an external site.) (see here for a list (Links to an external site.) of other ORF finders) to identify ORFs from the genome. Note that the EasyGene server can be very slow if your genome sequence is long. You can consider download the EasyGene package here (Links to an external site.) and run your local copy.

2. Compare your predictions with the output of the EasyGene tool and the ground-truth. Discuss your results (e.g. comparison of the length distribution; how many ORFs can be perfectly matched with known proteins; how many ORFs can be partially matched; what are the mistakes and think about whether we can make improvements in detecting ORF?)

3. Your group will need to present your findings in a recorded five-minutes talk uploaded in Zoom. Use up to four slides (to be submitted along with the individual submission) to the annotation of the genome that you are interested in exploring. Tell us about your predictions.

4. Choose a few ORFs your program predicted but not in the ground-truth annotation and use blastp on a browser here (Links to an external site.) or your local machines to align the ORFs to non-redundant protein database “nr” to find out if your prediction is potentially correct. 

5. One of your group members should submit your slides and the video.

Instructions:

1. Prepare your slides (~4 pages). You need to include the first page with a title introducing your group and the focus of your analysis. The remaining pages should describe your discussion about your results. (e.g. how many ORFs can be perfectly matched with known proteins; how many ORFs can be partially matched; what are the mistakes and think about whether we can make improvements in detecting ORF?) Your font size needs to be at least 12pt.
2. Record a video of the presentation of your slides. The video needs to be strictly less than 5 minutes. Your presentation will be shared with the class.

Submission:

1. The slides (~4 pages)
2. The recorded video of your group by one of your group members (<5 minutes)