Sample Paper - Computing - Dublin Institute of Technology

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Oct 1, 2013 (3 years and 9 months ago)

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W228
/407C




DUBLIN INSTITUTE OF TECHNOLOGY

KEVIN STREET DUBLIN 8

________________






BSc. (Honours) Degree in Computer Science




Year 4

_______________



Sample Paper

2012

____________



Bioinformatics




Mr. Denis Manley

Dr. D. Lillis

Mr. D. Treacy









Wednesday 18
th

January



4.00 p.m.


6. p
.m.

















Question 1 is
compulsory.

Answer any
two

of the other
questions.









W228
/407C

Q 1
.


(a)

Explain what attributes of Perl which make it
one of
the major programming languages
used in bioinformatics.

(10 marks)


(b)

Given the following

Fasta format

> Identifier], gene

name
, author, date of sequence analysis

(descriptor line)



lines of DNA sequences [ 60 characters in length]






Write a perl script that can



Extract the descriptor line
from
two

FASTA
formatted
file
s.

Extract DNA sequence

from
the file
s

and store in separate arrays
.

Determine
the comple
ment
ary strand for the first

DNA sequences extracted from
each file.

D
ete
rmine the ration of matches to non
-
matches

for
the
each of the primary

strands

[you can assume that the DNA sequences in both files are the same].

Print a report can will contain the following information:




The identifiers

and gene names in associated with each file




The degree of similarity between the sequences



Display i
n a suitable format the

primary

and
complementary

strands


associated with each file.


(30 marks)



Q 2
.


Explain the different types of
point mutations

and explain how
two

types,
x
-
linked

and
autosomal

mutations

can be
transmitted
from parents to their offspring, illustrating your
answer with a suitable example.


.
(
3
0

marks)




Q

3
.

A
bacterial genome

is very different from an animal genome discuss how these differences

cause the

transcription/translation of animal
gene
s to be more highly complicated that
transcription/translation in bacterial cells

(30 marks)



Q 4
.

Discuss
how

to
attempt to
find a
ge
ne’s
protein coding sequence

and its
core promoter

in a
eukaryotic genome.

(30 marks)



Q 5.

The dot plot, the PAM and the Bolsom

matrices are important tools in the measurement of
amino sequences similarity. Discuss how each can contribute to the determination of
sequence alignment similarity.


(30 marks)