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Multiple sequence alignment algorithms for the phylogenic analysis of chloroplast DNA

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Rumbold, A (2004) Multiple sequence alignment algorithms for the phylogenic analysis of chloroplast DNA. Honours thesis, University of Tasmania.

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Abstract

The application of approximate string matching and alignment algorithms to either
DNA or amino acid (protein) sequences is important for determining conserved
regions, functional sites and to allow for multiple sequence alignments from which
an evolutionary (phylogenic) tree may be inferred.
Global sequence alignment algorithms attempt to maximise the alignment score by
placing gaps (which are seen as insertion/deletion evolutionary events) in either
sequence so as to maximise the number of matching characters and minimise
mismatches and gaps. The extension of traditional dynamic programming
algorithms for aligning two sequences to aligning N sequences leads to a
polynomial increase in the space and time complexity. Consequently many
heuristic multiple sequence alignment algorithms, and improvements in the
representation of a multiple sequence alignment, have been developed. This
honours project has focussed on multiple sequence alignment algorithms, their
processing and space requirements and the suitability of the alignments of samples
of chloroplast DNA to further phylogenic analysis. Since the samples being used in
the analysis are hypervariable, this research has also looked at algorithms capable of
handling inversions in the DNA sequences (where a section of DNA has undergone
the mutation of reversing).

Item Type: Thesis (Honours)
Keywords: alignment algorithms, DNA, chloroplast, hypervariable, inversions
Publisher: Honours thesis, University of Tasmania
Additional Information:

Supervisors: Prof Arthur Sale and Dr Andrei Kelarev

Date Deposited: 26 Nov 2004
Last Modified: 18 Nov 2014 03:10
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