Difference between revisions of "Group project"

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<td>'''Name'''</td>
 
<td>'''Name'''</td>
 
<td>'''Name'''</td>
 
<td>'''Name'''</td>
 +
<td>'''Topic'''</td>
 
<td>'''TA'''</td>
 
<td>'''TA'''</td>
 
<td>'''Species'''</td>
 
<td>'''Species'''</td>
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<td>Herman Badwal</td>
 
<td>Herman Badwal</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
<td>Philip</td>
+
<td>Identify whether a human gene of interest may be involved in a disease</td>
 +
<td>Yaqi</td>
 
<td>''Aspergillus fumigatus'' (Af293)</td>
 
<td>''Aspergillus fumigatus'' (Af293)</td>
 
</tr>
 
</tr>
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<td>Yuanfan Yang</td>
 
<td>Yuanfan Yang</td>
 
<td>Marco Fiume</td>
 
<td>Marco Fiume</td>
<td>&nbsp;</td>
+
<td>Edwin Yip</td>
 +
<td>Use protein structural alignments for phylogenetic analysis</td>
 
<td>Boris</td>
 
<td>Boris</td>
 
<td>''Aspergillus nidulans'' (FGSC A4)</td>
 
<td>''Aspergillus nidulans'' (FGSC A4)</td>
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<td>Isuru Wijesoma</td>
 
<td>Isuru Wijesoma</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 +
<td>Protein structure prediction</td>
 
<td>Philip</td>
 
<td>Philip</td>
 
<td>''Candida albicans'' (SC5314)</td>
 
<td>''Candida albicans'' (SC5314)</td>
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<td>Alice Thach</td>
 
<td>Alice Thach</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
<td>Philip</td>
+
<td>Identify whether a human gene of interest may be involved in a disease</td>
 +
<td>Yaqi</td>
 
<td>''Candida glabrata'' (CBS138)</td>
 
<td>''Candida glabrata'' (CBS138)</td>
 
</tr>
 
</tr>
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<td>Vincent Leung</td>
 
<td>Vincent Leung</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 +
<td>Distinguish between structural and functional conservation</td>
 
<td>Philip</td>
 
<td>Philip</td>
 
<td>''Coprinopsis cinerea'' (okayama 7#130)</td>
 
<td>''Coprinopsis cinerea'' (okayama 7#130)</td>
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<td>Alexandr Bezginov</td>
 
<td>Alexandr Bezginov</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 +
<td>Predict protein/protein interactions for a gene of interest</td>
 
<td>Ryder</td>
 
<td>Ryder</td>
 
<td>''Cryptococcus neoformans'' (var. neoformans JEC21)</td>
 
<td>''Cryptococcus neoformans'' (var. neoformans JEC21)</td>
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<td>Hang Shi</td>
 
<td>Hang Shi</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
<td>Ryder</td>
+
<td>Predict protein/protein interactions for a gene of interest</td>
 +
<td>Philip</td>
 
<td>''Debaryomyces hansenii'' (CBS 767)</td>
 
<td>''Debaryomyces hansenii'' (CBS 767)</td>
 
</tr>
 
</tr>
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<td>Da Yu</td>
 
<td>Da Yu</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
<td>Ryder</td>
+
<td>Distinguish between structural and functional conservation</td>
 +
<td>Yaqi</td>
 
<td>''Giberella zeae'' (PH-1)</td>
 
<td>''Giberella zeae'' (PH-1)</td>
 
</tr>
 
</tr>
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<td>Shafa Chaudry</td>
 
<td>Shafa Chaudry</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 +
<td>Predict membrane topology</td>
 
<td>Ryder</td>
 
<td>Ryder</td>
 
<td>''Kluyveromyces lactis'' (NRRL Y-1140)</td>
 
<td>''Kluyveromyces lactis'' (NRRL Y-1140)</td>
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<td>Miao Yu</td>
 
<td>Miao Yu</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
<td>Yaqi</td>
+
<td>Predict membrane topology</td>
 +
<td>Ryder</td>
 
<td>''Magnaporthe grisea'' (70-15)</td>
 
<td>''Magnaporthe grisea'' (70-15)</td>
 
</tr>
 
</tr>
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<tr class="s0">
 
<tr class="s0">
 
<td>'''Methionine'''</td>
 
<td>'''Methionine'''</td>
 +
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
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<td>Alex Ling</td>
 
<td>Alex Ling</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 +
<td>Identify whether a gene of interest has been under recent positive selection</td>
 
<td>Yaqi</td>
 
<td>Yaqi</td>
 
<td>''Pichia stipitis'' (CBS 6054)</td>
 
<td>''Pichia stipitis'' (CBS 6054)</td>
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<td>Jennifer D'Cruz</td>
 
<td>Jennifer D'Cruz</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
<td>Yaqi</td>
+
<td>Distinguish between structural and functional conservation</td>
 +
<td>Philip</td>
 
<td>''Schizosaccharomyces pombe'' (972h-)</td>
 
<td>''Schizosaccharomyces pombe'' (972h-)</td>
 
</tr>
 
</tr>
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<td>Dilpreet Dhesi</td>
 
<td>Dilpreet Dhesi</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
<td>Yaqi</td>
+
<td>Identify and contrast conserved regions on a gene vs. conserved regions on its expressed protein</td>
 +
<td>Ryder</td>
 
<td>''Ustilago maydis'' (521)</td>
 
<td>''Ustilago maydis'' (521)</td>
 
</tr>
 
</tr>
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<td>Linda Zhao</td>
 
<td>Linda Zhao</td>
 
<td>Zhongyuan Zhang</td>
 
<td>Zhongyuan Zhang</td>
 +
<td>Identify and contrast conserved regions on a gene vs. conserved regions on its expressed protein</td>
 
<td>Boris</td>
 
<td>Boris</td>
 
<td>''Yarrowia lipolytica'' (CLIB122)</td>
 
<td>''Yarrowia lipolytica'' (CLIB122)</td>
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<tr class="s1">
 
<tr class="s1">
 
<td>'''Serine'''</td>
 
<td>'''Serine'''</td>
 +
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
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<tr class="s0">
 
<tr class="s0">
 
<td>'''Threonine'''</td>
 
<td>'''Threonine'''</td>
 +
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
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<tr class="s1">
 
<tr class="s1">
 
<td>'''Valine'''</td>
 
<td>'''Valine'''</td>
 +
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
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<tr class="s0">
 
<tr class="s0">
 
<td>'''Tryptophan'''</td>
 
<td>'''Tryptophan'''</td>
 +
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
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<tr class="s1">
 
<tr class="s1">
 
<td>'''Tyrosine'''</td>
 
<td>'''Tyrosine'''</td>
 +
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>
 
<td>&nbsp;</td>

Latest revision as of 19:32, 20 November 2008

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