26 Jun CSE5BIO Bioinformatics Technologies Sem 1 2015, Assignmen
Question
CSE5BIO Bioinformatics Technologies
Sem 1 2015, Assignment One 20 Marks
(Due Thursday 16 April 2015)
Copying, Plagiarism:Plagiarism is the submission of somebody else’s work in a manner that gives theimpression that the work is your own. The Department of Computer Science and Information Technology at La Trobe University treats plagiarism very seriously. When it is detected, penalties are strictly imposed.
Computer Science and Information Technology Professionals are being employed in many diverse areas of Science. In this subject we are focussing on Bioinformatics and the knowledge and skills that you will require to understand and participate in this field of research or as an advance step to greater employment opportunities. This assignment will help you to clarify the fundamentals of Bioinformatics from the end user perspective and allow you to participate in information gathering.
Biology can be seen as an information transfer chain, it is our business to deal with this information in all its biological encoding and higher order significance. The ‘central dogma’ is the key information pathway in biology as shown in Figure.
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These three biological molecules form the basis for much of bioinformatics, therefore understanding the importance, use and storage of this data is essential. This chart, in Q1 you can use as reference for later work in the course or future research.
Q1. Complete the chart on the following page (Table 1). In each of the blank sections fill the following
(8 Marks)
a) Provide a brief description of each molecule in question. What is their role and importance in the central dogma?
b) List 3 primary data resources (Biological databases) for each molecule with their respective URLs.
c) State 3 types of analysis those are appropriate to the molecule from the Bioinformatics viewpoint. e.g. sequence alignment,
d) List one tools for each analysis listed with their respective URLs. e.g. BLASTN for DNA alignment.
Q2. Bioinformatics is an intelligent method for obtaining biological knowledge using computationaltechniques. In this question you will execute a workflow to produce a biological outcome.
(12 Marks)
We will investigate Leukaemia in humans with reference to the B-cell lymphoma 2 (BCL 2) group of protein.
a) Using the NCBI Gene Database, investigate BCL 2: search ID PPP1R50. This display has a lot of information, list the information you infer about the particular gene.
• Brief Summary of the gene (In your own words).
• Genomic context.
b) Scroll to the (NCBI Reference Sequences) section and click the protein sequence (NP_000624.2). You will be taken to the entry in NCBI Protein. Select “FASTA”, Click ‘Send to File’ to save the protein sequence.
• Paste your sequence into the structure model server http://swissmodel.expasy.org/interactive. 3D structure of your protein will be generated. Provide the screenshot of your result page.
• Retrieve the PDB file and save it. Open the protein structure using RasMol, save the image as GIF and paste it in your report.
c) Go to NCBI BLAST www.ncbi.nlm.nih.gov/blast. Select ‘protein blast’ and paste the protein sequence saved from Q2b. Execute the search with the ‘swissprot’ database.
• Pastes the results obtained into your report and provide a brief analysis of the result.
• The coloured lines indicate the coverage and quality of alignments of other proteins in the database to your query. Translate the scientific name of five matching sequences organisms into common names e.g. Homo sapiensà human.
d) Scroll down your BLAST result page to find the match to Xenopus laevis (African Frog). Click the accession link corresponding to Xenopus laevis.
• Download the protein sequence as before, generate a 3D model using Swiss Model, load it in RasMol, save the image as GIF and paste it in your report.
• Compare it with the human protein structure generated in Q2b, what do you observe by comparing two structures?
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