Group project

The Group Mini-Project

   

You have been assigned to groups of three or four students.

Each group will take on one workflow to annotate. As a group, you will jointly define and structure the workflow. Individually, you will annotate some of the data items or procedures of the workflow. Your mark will be based on both components.

The project will proceed as follows:

1. A number of topics from the general area of functional annotation are listed in the table below.
2. Jointly, as a group, choose one of the topics and one alternative (in case too many groups choose the same topic). If you would like to propose a different topic you are interested in, you may do so.
3. Discuss within your group your understanding of the topic, what databases and tools could be relevant and a proposed process - a sequence of steps - to address the topic. You may involve your TA into the discussion at any time.
4. Plan your time to be able to communicate about the project within the group, go through some improvements, and finish by the due date.
5. Summarize the results of the discussion (your plan how to go about this) in a paragraph of text, and e-mail it to your TA for feedback and iterated improvements.
6. Once the improvements are done, the following milestones should be achieved:
   1. Task is broken down into a number of procedures
   2. Each procedure has clearly defined input data, an algorithm operating on that data, and output data
   3. There is a designated group member for each procedure
   4. The entire process has been summarized in approximately one page, jointly written.
7. Individually, describe your designated procedure(s) in approximately one page. Define input data, algorithm, parameters, alternatives, output data etc. Give references. You may request feedback from TAs and from your group members and classmates. However you will take author's responsibility for the result.
8. Submit a collated hardcopy of the process summary and your individual procedure descriptions by the due date. Make sure your individual contributions are clearly identified with your name.

The due date is Thursday, December 4. (last day of class) at 6 p.m.

---

Topics

• Identify and contrast conserved regions on a gene vs. conserved regions on its expressed protein
• Distinguish between structural and functional conservation (1, 2, 3)
• Predict domain boundaries (1, 2)
• Identify whether a gene of interest has been under recent positive selection (1, 2)
• Obtain a profile/profile alignment of distant homologues (1, 2)
• Identify whether a human gene of interest may be involved in a disease (1 2)
• Calculate a column-wise conservation score (1, 2)
• Predict membrane topology (1)
• Predict protein/protein interactions for a gene of interest (1 2)
• Identify and evaluate linear sequence motifs (1, 2)

(Some PubMed links are provided to get you started. Make use of the "Related Articles" feature in PubMed.)

---

Groups

Group	Name	Name	Name	Name	Name	Topic	TA	Species
Alanine	Maria Soloveychik	Alison Muir	Zarnaben Shah	Herman Badwal		Identify whether a human gene of interest may be involved in a disease	Yaqi	Aspergillus fumigatus (Af293)
Cysteine	Yuan Yao	Adam Santoro	Yuanfan Yang	Marco Fiume	Edwin Yip	Use protein structural alignments for phylogenetic analysis	Boris	Aspergillus nidulans (FGSC A4)
Aspartate	Nikko Torres	Natalia Thawe	Marja Cemma	Isuru Wijesoma		Protein structure prediction	Philip	Candida albicans (SC5314)
Glutamate	Joyce Lam	Leo Wan	Ying Zhu	Alice Thach		Identify whether a human gene of interest may be involved in a disease	Yaqi	Candida glabrata (CBS138)
Phenylalanine	Bell Ho	Kris Hon	Jason Yau	Vincent Leung		Distinguish between structural and functional conservation	Philip	Coprinopsis cinerea (okayama 7#130)
Glycine	Fan Zhang	Fang Cai	Greg Clark	Alexandr Bezginov		Predict protein/protein interactions for a gene of interest	Ryder	Cryptococcus neoformans (var. neoformans JEC21)
Histidine	Yi-an Chen	Rachel Ford	Kiera Clayton	Hang Shi		Predict protein/protein interactions for a gene of interest	Philip	Debaryomyces hansenii (CBS 767)
Isoleucine	Eric Wong	Louis Barbier	Youssef Youssef	Da Yu		Distinguish between structural and functional conservation	Yaqi	Giberella zeae (PH-1)
Lysine	Wasan Abada	Madhavi Patel	Jing Huang	Shafa Chaudry		Predict membrane topology	Ryder	Kluyveromyces lactis (NRRL Y-1140)
Leucine	Wei Tang	Rui Chen	YinYing Zhang	Miao Yu		Predict membrane topology	Ryder	Magnaporthe grisea (70-15)
Methionine								Neurospora crassa (OR74-A)
Asparagine	Devin Trudeau	Julia Li	Jiayi Hu	Alex Ling		Identify whether a gene of interest has been under recent positive selection	Yaqi	Pichia stipitis (CBS 6054)
Proline	Jestyn Liew	Curtis Foong	Maryam Foumani	Jennifer D'Cruz		Distinguish between structural and functional conservation	Philip	Schizosaccharomyces pombe (972h-)
Glutamine	Anand Iyer	Kevin Lau	Cecilia Chan	Dilpreet Dhesi		Identify and contrast conserved regions on a gene vs. conserved regions on its expressed protein	Ryder	Ustilago maydis (521)
Arginine	Cheng Yu	Risa Yuk Low	Lakshmi Sugavaneswaran	Linda Zhao	Zhongyuan Zhang	Identify and contrast conserved regions on a gene vs. conserved regions on its expressed protein	Boris	Yarrowia lipolytica (CLIB122)
Serine
Threonine
Valine
Tryptophan
Tyrosine