W228/407C
DUBLIN INSTITUTE OF TECHNOLOGY
KEVIN STREET DUBLIN 8
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BSc. (Honours) Degree in Computer Science
Year 4
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Sample Paper 2012
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Bioinformatics
Mr. Denis Manley
Dr. D. Lillis
Mr. D. Treacy
Wednesday 18th 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 files.
Extract DNA sequence from the files and store in separate arrays.
Determine the complementary strand for the first DNA sequences extracted from
each file.
Determine 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 in 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.
.(30 marks)
Q 3. A bacterial genome is very different from an animal genome discuss how these differences
cause the transcription/translation of animal genes to be more highly complicated that
transcription/translation in bacterial cells
(30 marks)
Q 4. Discuss how to attempt to find a gene’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)