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Term Project
Audio recording of this Discusion session about the Term Project
Description |
The term project is due April 24th, in class at 11:20pm and is worth 100 points. Students are
encouraged to help each other on the project, but must turn
in only their own work.
The term project is a molecular phylogenetic analysis of at least one
unknown specie isolated in lab. Each student has isolated at least
a couple of organisms from their own samples, then attempted to
amplify ssu-rDNA from some of these. Any of these that contained
an appropriate-sized PCR product (1kbp) were sent to Eurofins/MWG/Operon in Huntsville, Alabama
for sequencing with 515F, one of the primers used to obtain
the DNA by amplification. These sequences are the starting point
for a molecular phylogenetic analysis. |
Requirements |
The term project you turn in must contain the following items
- THIS IS A CHECKLIST! Each of the major headings below are links to detailed directions for that section.
- Your data
- A summary of the microbiological information about your isolates.
- Printouts of the raw data from your sequencing reactions
(the .pdf files)
with the reliable region of this sequence (from the .clip file) highlighted.
- An database search with your sequence
- A printout of the Sequence Match results.
- A printout of the sequence(s)
most similar to yours identified in this Sequence Match.
- A printout of the Classifier results.
- A phylogenetic analysis of your sequence(s)
- An phylogenetic tree containing your sequence(s) and representatives from major bacterial phyla, with your sequence highlighted
and each phylogenetic group indicated.
- A final tree containing your sequence(s), the sequences closely related to your sequences, and other representative sequences, with your sequence highlighted
and each phylogenetic group indicated.
- The Writeup
- Introduction
- Results
- Discussion
- Citations
|
Grading |
Data
|
Microbiology |
Basic - 3 |
5 |
10
|
100
+2 for computer
help referals
|
| Details - 2 |
Chromatogram |
Printout - 3 |
5 |
| Highlighting - 2 |
Database Search
|
SeqMatch
|
Printout - 5 |
10
|
15
|
| Closest relatives - 5 |
Classifier |
Printout - 5 |
5 |
Tree Construction
|
Phylum tree |
Sequence choices - 10 |
20 |
40 |
| Root - 3 |
| Highlighting - 2 |
| Annotation - 5 |
Final tree |
Sequence choices - 10 |
20 |
| Root - 3 |
| Highlighting - 2 |
| Annotation - 5 |
Write-up
|
Intro |
Subjective - 30
A+ work : -30/30
A- work : 27/30
B+ work : 24/30
B- work : 21/30
C+ work : 18/30
C- work : 15/30
D work : 12/30 |
30
|
35
|
Results |
Discussion |
Citations |
Basic (1-2 refs) - 3
(RDP, MB451 excluded) |
5 |
| Complete (>2 refs) - 2 |
|
|
| Last updated
April 30, 2009
by James W Brown |