Solved by a verified expert: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.
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?
—-
End
of Question—-
Table 1.Bioinformatics Data and
Resources
DNA
RNA
Protein
A. Role & Importance
B. Resources with URL
C. Types of Analysis
D. Tools used for analysis with URL
Recent Comments