Here are a few comments about what I'd like to see in final reports.

1) Your paper should have a title, a one-paragraph abstract, titled sections,
   and bibliographic references.  It should be 8-12 pages long in 12pt
   type.

2) Something that is key to keep in mind, no matter what you are writing,
   is "who is my intended audience"?  It's surprising how often even
   professional researchers lose track of this.  For your project report,
   you should pretend that your audience is your fellow students in the class.
   That is, you should assume that your readers have about the same general
   background in bioinformatics that you do, but that they don't know
   as much about the topic of your project as you do.  Therefore, you should
   describe your algorithms, data sets, etc. accordingly.

3) Your paper should probably have sections along the lines of:
   - Introduction: what you attempted to do and what the motivation is.

   - Approach: what you did.  If you developed your own approach, you should 
     describe your work in sufficient detail that someone else could replicate 
     your work.  If you are using previously developed algorithms, describe
     them briefly, and provide references to complete descriptions.  
     Don't describe your code organization or implementation details.  For the 
     intended audience, you should assume that interested readers could 
     figure out how to implement the code as long as the algorithm is 
     described in sufficient detail.

   - Empirical Evaluation: describe your experiments and results.
     Describe your data sets in adequate detail.  How many sequences, profiles,
     etc. does it encompass?  If you selected a subset of a larger data set,
     how did you make this selection?  Describe how you chose settings for
     parameters of the algorithms?  Clearly state what are you trying to 
     test/demonstrate in your experiments.  It's nice to have one or
     more explicitly stated hypotheses or questions.

   - Analytical Evaluation: if relevant, describe your proofs or other
     formal results (few papers will have this section).

   - Discussion: discuss your results.  What are the lessons of your
     experiments?  What are the limitations of your approach?
     What would you suggest for future work in this direction?

  You don't have to strictly adhere to this format if you think it is
  not the best organization for your particular project.

4) Every paper should have some figures or tables.  All figures and tables
   should have informative captions.  If you include graphs, make sure
   that the axes are labeled.  Figures and tables should be referenced
   and described in the text, not just dropped into the document.

5) Finally, if your project involves empirical work, don't worry if your
   experiments don't turn out as you predicted.  That's how science
   often goes.  Data have a way of frequently humiliating hypotheses.
   The important thing is how well you carried out the process.  That is,
   you will be graded on such things as (i) clearly defining your objectives/
   hypotheses, (ii) selecting appropriate experiments, (iii) clearly reporting
   relevant results, and (iv) carefully discussing the significance/lessons
   of your results.