Instructions
Example sequence
Example sequence Repeat-masked

Example sequence, RepeatMasker output summary
Example sequence, RepeatMasker output table of repeats
Example sequence, blastn output, query on nr database
Example sequence, Genome Browser output

GenSeq1All
GenSeq1RM
GenSeq2All
GenSeq2RM

If you wish to revise your genomics project report, you may do so. These revised project reports are due Nov. 08 (Friday). Please turn them in to Cathy on that day (not before or after). She made very specific comments and recommendations, and I urge you to respond to them. The following is a message from her with more detail on the grading and the revisions.

Hi Everyone,
The grading scheme for the reports was as follows:

4 points for each question in Section 1 (2 points per sequence)
4 points per question in Section 2 (again, 2 points per sequence)
4 points per question for the first 4 questions of Section 3; then 10 points for the summary discussion
30 points for the discussion.

The majority of students scored above an 80%, with most of the scores from 80-86.  Most students who scored lower omitted sections of the report.  The most common cause of missed points was the content of the discussion section.  We would like you to go beyond a simple summary or a brief OMIM output, but rather go more in-depth into areas of interest.  Good items to include in yor discussion are a comparison of features of the two sequences, points that interested you during your exploration, and/or an analysis of the accuracy of GenScan output.  We will be expecting at least 2 pages (it depends on the overall amount of discussion in the whole report as well). [Note - a few more ideas are listed below.]

The resubmissions will be due on Nov. 8th at the end of class. You should turn in both the original report and the revised/corrected report. Make the corrections on a separate sheet. If you change only one section (e.g. the Discussion) you can turn that in as your revised report along with the original report. However, if changes are made in multiple places, you should turn in a complete revised report (along with the original). You may want to respond to my comments by explaining how you have revised the report in response to the critique.  Attach this sheet to your original report.  If you do not wish to resubmit, turn in on that day a sheet with your name and project grade to confirm that you are satisfied with your score.  I would like everyone to wait until that day to turn them in so that they can be collected and returned all at once.  If you have any questions, see me in my office hour.  If this time does not suit, email me so we can work out a meeting time.

Cathy

Additional/expanded ideas for interesting Discussion:

Compare the results for the two genes. They differ in almost all aspects:
 GC content
 Types of predominant repeats
 Amount of sequence that aligns
 Etc.

Compare the Genscan predictions with the known exons.

Compare the status of the genes and the maps in the genome project. Are both in RefSeq? The data in the databases and browsers is not perfect and never will be. How do you resolve conflicting and difficult-to-explain results? Examples include the same exons assigned to different genes, and apparent gene duplications when for genes whose mutations lead to recessive phenotypes.

Contrasts in the mechanisms of the pathophysiology.

What did you learn about gene expression, and the pathways for expressing the two genes? Are the same promoters and splice junctions used in all tissues?