You will be assigned 5 protein sequences, some of which were translated from ESTs from a vertebrate organism. As soon as possible after receiving your assignment (NOT the day before the term paper is due ;-), download your sequences to your own computer.

Because these proteins are based on ESTs, there may be errors in the sequences and some may be truncated at their N and/or C termini. These sequences are part of a UM research project. A UM faculty member in a biological science wants to know which ones are worthy of experimental study. He is especially interested in unknown or conserved hypothetical proteins.

You are to correctly classify each sequence as "known", "conserved hypothetical" or "unknown". For "conserved hypothetical" and "unknown" proteins, predict as much as you can about their secondary and tertiary structure and possible function. For "known" proteins, give the name of the protein family, describe the evidence that the sequence is a member of that family, and briefly describe the functional and structural attributes of that family, up to and including any known tertiary structures. For each "conserved hypothetical or quasi-hypothetical", list all other members of the group, describe the evidence that the sequence is a member of the group, give all the functional or structural annotations ascribed to any member of the group, and state whether any of these annotations should be assigned to your protein.

Use any techniques, in GCG or on the Internet, to make your predictions. This demonstrates your knowledge of course materials and your ability to use the literature and computer tools in this area, using both GCG and web resources, as appropriate. Each person will analyze a different set of sequences. Each person must do his or her own analyses and write his or her own paper, but you can freely share techniques, websites, etc. Send any interesting info to the class email list. Use the list to ask (and answer) questions regarding analyses too.

Write up your work in the form of a short (5-10 page narrative excluding tables, figures, or references, double-spaced, 12 pt font, 1 inch margins) scientific paper, following instructions to authors for any one journal that publishes papers of this type. This paper is due before class on Tuesday, December 12, 2006.

E-mail the abstract of the paper to the class list on that date and prepare a 5-minute presentation (and only ONE transparency) to summarize the interesting parts of the paper.

The paper should include:

Abstract (150 words or less)

Introduction: Set the stage for your analyses, describing why one would want to analyze ESTs, and introduce the different types of computational techniques you used.

Materials and Methods: Describe the computer and manual tools and methods you did use to make your predictions, including authors, versions, URLs.

Results: Describe the predictions you can make about your protein sequences: secondary and tertiary structure, including motifs and domains, structural class, predicted strucure, and protein family. Include tables and/or figures if appropriate.

Discussion: On what do you base your predictions? Discuss all evidence pro and con for the functions and secondary and teriary structures you predict. Include tables and/or figures if appropriate.

Conclusions: All that you can conclude from this project.

References: Include ALL authors in references. Correctly cite any Web resources you use. Use a consistent reference format from a journal in the field.

It is NOT required that the term paper for this one-semester course be publishable. But try your best!