Undergraduate Bioinformatics Report Guidelines

This report is worth 30% of the final marks for the course.

The report is to be submitted through the Turnitin Assessment task dropbox. Make sure you submit by the due date. Late submission will be penalised at 2 marks per day. Extensions only by Special Consideration application.
Your Turnitin matches with published sources will be checked. Note that inadvertent matches such as sequences, common phrases and references will be ignored. However, pasting text and subsequently rearranging it is detectable, and is plagiarism and you will be penalised.

This report comprises two sections. The first is a section designed to test your theoretical knowledge, and the second your practical skills.

Section A
Describe some of the ways that Bioinformatics is used to facilitate scientific discoveries. This can be fundamental science, or new applications. Use at least three specific examples from the literature. This might include such things as elucidating protein function, using microarrays for target discovery or diagnosis, mining literature for novel information, drug discovery etc. Write approximately 1000 words, use figures (attributed) and give references. The first paragraph should be a brief introduction, followed by the specific examples.

Section B
Look in the “Sequence Allocation” file to find the sequence allocated to you. It is the row number next to your student number. Open the appropriate “Sequences for report” files (open the one with your number). Use copy and paste to place your sequence in its own document, save it and work with that sequence only. The starting premise of your report is that you have cloned the gene and obtained the sequence of it. The task of your report is to analyse the gene in any and all ways that you can. This means that you will use the bioinformatics analysis tools that you have used in class, and produce a final report that describes the gene and its product in detail. This includes, but is not limited to, encoded protein, homologs in other species, evolutionary tree (build your own), chromosomal location, gene structure, relationship to inherited disease, protein structure etc. Note that each of the sequences may encode more than one reading frame, however (hint!) in all cases the longest reading frame is the one to analyse.

The report should be descriptive, and show that you understand the principles behind the analysis tools you have used. Results (e.g. ORF finder output, BLAST search outputs, phylogenetic tree, protein structural display etc) should be included as appendices.

Format these correctly, for inclusion in a word document. This means changing margin sizes, and using Courier (or another non-proportional font) etc. You can also paste screen shots into your document. As to the layout of the report, I suggest the following.

Part 1. Analysis of the sequence. List the steps you went through to identify the gene and encoded protein. List the tools that you used, what the parameters used were and what the findings were for each step. The URLs of the tools you used should be listed here. You may add diagrams here, but not too many. The raw data you obtain should be added as an appendix (don’t add many pages of output however, just an example of the output from each tool you used. For example, just add the first page of a BLAST output, not the entire file). In this section, refer to the results in the appendix, so each appendix should be numbered.

Part 2. Several paragraphs that summarise the literature relevant to the identified gene/protein. This should be referenced in “literature review” style, but is not meant to be a full literature review. Just discuss the relevant literature. The material for this section should be sourced from a variety of databases, but must be summarised in your own words. Material that should be discussed here may include the function of the gene/encoded protein, any relationship to disease, any mutations identified etc.

Part 3. Bibliography/references. Both URL’s and literature should be cited, under separate headings.

Part 4. Appendices. Numbered appendices documenting your analysis results.

Assessment

INTRODUCTION (Section A) (Out of 8)
Must cite some original literature from PubMed.

TOOLS USED and Discussion of Findings (Section B Part 1) (Out of 6)
Use all the tools you have learned in the course.

ANALYSIS DATA (The data presented in Part 4, appendices) (Out of 6)

LITERATURE REVIEW (Section B Part 2) (Out of 6)
Review the function of the protein encoded by your gene. Include any reference to inherited genetic disorders.

PRESENTATION/LAYOUT/ORGANISATION OF THE REPORT/REFERENCES (Out of 4)