Download 12 BOC314 Practical 1

PRACTICAL COURSE
BOC314
INTRODUCTION TO BIOINFORMATICS
INTRODUCTION
Biological data and DNA sequence data in particular, are accumulating at a phenomenal rate. The DNA
sequence of the complete human genome has been determined. Although this achievement seems like an
end in itself, in reality it is only the beginning. In order to exploit the wealth of DNA sequence and other
biological data, a new science has arisen that fuses biology with mathematics and computer science –
‘bioinformatics’.
To find the genes within the genomic sequence is a massive task in itself. Once apparent, otherwise
uncharacterised coding regions must be assigned a function. Thereafter, the interactions between genes
and gene products must be understood at all levels, not merely in the context of the pathways within and
between cells but also in terms of the evolution of gene families within and between species. These
questions can all be addressed using bioinformatics.
Bioinformatics touches all of biology, and straightforward access to data via the Internet means that a
wealth of information is available, literally at our fingertips. However the newcomer to bioinformatics
might be discouraged because of the initially daunting computational and mathematical content. Others
might simply be confused by the language and terminology of bioinformatics.
To help overcome these barriers, we will examine this novel and rapidly evolving scientific discipline
during our practical classes. The concepts will be explained and practical examples of how the immense
store of data can be exploited will be provided.
During five practical sessions we will learn how to access and search for information using appropriate
retrieval systems of particular relevance to molecular biologists.
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BOC314 PRACTICAL 1
RETRIEVING AND ANALYSIS OF NUCLEOTIDE SEQUENCES USING ENTREZ
Method
1.
Open a new word document and type in your Full Name, Student Number, Date as well as
BOC314 Practical No 1 at the top of the document. Save the file using your last name followed
by your initials and the number 1 (indicating practical 1). For example: MalemaJ1 (for Julius
Malema practical 1)
2.
Open Internet Explorer browser by double clicking on its name:
3.
Type the following address in the location box: http://www.ncbi.nlm.nih.gov and press enter.
4.
Click on Nucleotide (link on right hand side of screen under Popular Resources). In the “Search”
box, maintain the Nucleotide search option, and type the name of the gene you will be searching
for into the “Search” box. Click on Go. We shall search for the following two genes (the one after
the other). Type the following words:
a)
Aeromonas trota
A number of sequences will be displayed. Scroll down until you find one with the following
description; Aeromonas trota preproaerolysin gene. (Note: if none of the sequences on
the page corresponds to the required gene, click on ‘next page’ until you find the correct
sequence).
b)
Neisseria gonorrhoeae strain CH811
Select the sequence with the description Neisseria gonorrhoeae strain CH811 MinCDE
gene cluster
5.
Copy all the information of the two gene sequences to the word document: Select the part that
you copied and change the font to Courier New, font size 9 and the paragraph spacing to
single line spacing (important).
6.
Remember to frequently save the word document on your storage device.
7.
To find a paper (article) related to the gene maximize your search results again, click on the 1st
“PUBMED” (blue font) link.
SAVE the information displaying only the journal reference,
article title, author(s), and abstract on your storage device, in the same way that you have
saved your sequence data.
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REPORT
Compile a neat report consisting of the following in sequential order in a single word document:
The name of the file containing your report should be your last name followed by your initials
and the number 1 (indicating practical 1)
For example: MalemaJ1 (for Julius Malema practical 1)
Files that are not in this format will not be marked
1. The sequence information of the Aeromonas trota gene.
o
Highlight the following on the DNA sequence using the colours as indicated for
each element:

Ribosomal binding sequence

-35 transcription sequence

-10 transcription sequence

translation start codon

translation stop codon
2. Pages with questions and answers completed in full.
3. Summary of related article (only the journal reference, author(s), and abstract)
4. The sequence information of the Neisseria gonorrhoeae gene cluster.
o
Highlight the following on each sequence

NOTE: the sequence contains three genes in a cluster; understand the
following concepts before attempting this section –

Unidirectional gene overlapping,

Alternative start codons.

-35 transcription sequence

-10 transcription sequence

translation start codon

translation stop codon
5. Pages with questions and answers completed in full.
6. Summary of related article (only the journal reference, Article title, author(s), and
abstract)
Total marks = 61
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BOC314 PRACTICAL 1 GENE ONE
RETRIEVING AND ANALYSIS OF NUCLEOTIDE SEQUENCES USING ENTREZ
Student Number
:
_____________________________
Name
:
_____________________________
.
Question 1
What is the abbreviation of the FIRST gene you have retrieved?
Answer 1
_______________________________________________________________
Question 2
What is the accession number of the above gene?
Answer 2
_______________________________________________________________
Question 3
What does this gene code for?
Answer 3
_______________________________________________________________
_______________________________________________________________
Question 4
In which Scientific Journal was an article published with respect to the cloning of this
gene??
Answer
Name of Journal (Full name not abbreviation) ___________________________
Volume of Journal
_______________________________________________
Date of Journal (Month + year)_______________________________________
Title of article
_______________________________________________
_______________________________________________________________
_______________________________________________________________
_______________________________________________________________
_______________________________________________________________
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BOC314 PRACTICAL 1 GENE TWO
RETRIEVING AND ANALYSIS OF NUCLEOTIDE SEQUENCES USING ENTREZ
Student Number
:
_____________________________
Name
:
_____________________________
Question 1
What is the abbreviation of the SECOND gene you have retrieved?
Answer 1
_______________________________________________________________
Question 2
What is the accession number of the above gene?
Answer 2
_______________________________________________________________
Question 3
What was the effect when minC was inactivated in N. gonorrhoeae CH811?
Answer 3
_______________________________________________________________
_______________________________________________________________
Question
What effect did an insertional mutation of MinD have on N. gonorrhoeae?
Answer
_______________________________________________________________
_______________________________________________________________
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