Bioinformatics DT249 4 Assignment 2

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Dec 13, 2013 (3 years and 7 months ago)

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Bioinformatics DT249

4
Assignment

2

Using the Human leckocyte elastase gene (about ~5000 bp)


Write a paper of approximately 2
000 words, not inclusive of
any
perl
code
/algorithm pseudocode
,
on:


Download the FASTA DNA file and the FASTA amino

acid file for the above gene.

1.


Using you perl
scripts

translate the DNA sequence overall reading frames. Design an
algorithm that can find alignment between the “translated” sequences and the
experimental determined amino acid sequences.


(10 marks)



2.

Using online analytic
al tools and /or a perl scripts
determine

regions of alignment

between the amino acid translated DNA sequences and the experimentally obtained
:
amino acid sequences: specifying
their position

(bp number);

the
reading frame and any
othe
r data you cons
ider will be critical the
annotation

of the
gene

sequence.



(15 marks)

3.

Using the known annotated data in the
geneback record
: Discuss

the results of your
analysis
:

the
“correctness” of
the exon
and
intron positions
; the codon start position
s
and other regions you consider important to the DNA/amino acid sequence analysis.




(25

marks)


The paper must have the following sections
1
:



an introduction,



sections that answer the above questions,



conclusion



reference


The
paper

called
an

Analysis

of the

DNA and Amino Acid sequence the human leukocyte elastase
gene”.
must be

emailed to
denis.manley@dit.ie
, by:
13
th December 2012


Late Submissions

Any assignments that are submitted after the due date but w
ithin one working week will be
Marked
out of 50%.
Assignments submitted more than one week late will receive a mark of zero.
There will
be no extensions granted

unless a person has been out for the period of the assignment and can
furnish proof of their
absence.




1

If you have any questions in relation to what you should have in these section or any
questions on your
interpretation of question contact me.