CSC8312 -- Bioinformatics Theory and Applications

New

The IDs are now available.

This assignment is designed to test your ability understand and computationally derive useful biological information from a DNA/Protein sequence. You will need to write a short report on protein sequences that you have been given, checking the annotation, the genomic context and sequence features.

You will be provided with Uniprot IDs for 4 proteins, from different organisms. You should pick 1 proteins from these 4; you should do an initial analysis and then pick the one you think is most interesting. You need to write a short report on it, checking the accuracy of the Uniprot record, and providing evidence for as many of the statements in the record as possible.

In particular, you should:

• Retrieve the nucleotide sequence of the genomic segement from which the transcript is derived. You will need to retrieve upstream and downstream sequence also.
• Using relevant tools, check whether predicted coding regions correspond to the amino acid sequence of hte protein when translated, identifying relevant introns and exons if possible. Do not rely on the annotations in the EMBL/GENBANK records, but reproduce the results.
• Check any genomic features that you can find in the genomic DNA records, and see which tools predict these computationally.
• Many Uniprot records have functional assignments. Using appropriate tools, report on whether you agree with this functional assignment.
• For those records with associated publications, what is the relationship between the sequence and the publications.

Deliverables

A finished paper produced in the style of a Bioinformatics paper. You can see some examples of the style at http://www.oxfordjournals.org/bioinformatics/for_authors/general.html

The paper should obey a strict 6 page limit. People exceeding this page limit will be penalised. You must obey the style guide lines for bioinformatics — you should not shrink font sizes.

Marks will be given for scientific writing style (10%), background (10%), methods (35%), results of analysis (30%) and discussion of the results(15%).

In particular, additional marks will be award for:

• The application of a wide range of bioinformatics tools. The discipline is constantly growing and changing. We do not teach all the tools that you should be aware of.
• You should record your work, and the methods that you have used accurately and consistently.
• The reasons for any conclusions you make should be described accurately. It is as important to know why you have concluded something as what you have concluded.
• You should present the work in as concise a manner as possible. Use tables, figures and graphs wherever appropriate.
• Adequate references and reference lists.