This work addresses two areas of computational biology: automation of sequence
processing and an assessment of the evidence for a hypothesized salmonid
genome based on an analysis of a set of expressed sequence tags.
Three problem areas in sequence processing are addressed in the first half of
the work. Chapter 3 describes an accurate technique for trimming of vector,
adapter and poly(A) sequence. Chapter 4 suggests methods for verifying the
accuracy of assembled mRNA transcripts despite a large number of
chimeras in the cDNA clone libraries. Chapter 5 is concerned with the problem
of estimating the number of transcripts in a tissue or cDNA library, concluding
that computational and statistical techniques are inadequate to estimate the
quantity accurately.
The hypothesized salmonid genome duplication has been widely accepted since
1984. If it occurred, it should have left evidence in the form of many
paralogous pairs of genes, all at approximately the same degree of sequence
divergence. To assess this question, several hundred thousand ESTs were
assembled into transcripts, compared to each other to find homologs, and
the evolutionary distances of the homologs represented as a histogram.
Evidence of a single evolutionary event was not seen. The same procedure
was applied to Xenopus laevis, which has a well-established recent
genome duplication, and Danio rerio, which is known not to have had
one. In those cases, the evidence for or against a genome duplication
appeared exactly as predicted. The conclusion is that if the salmonid
genome duplication occurred, some force altered its evolutionary development
subsequently to mask the duplication, but also that a genome duplication is not
necessary to explain the observed pattern of homolog distances.
| Identifer | oai:union.ndltd.org:uvic.ca/oai:dspace.library.uvic.ca:1828/331 |
| Date | 01 April 2008 |
| Creators | Brown, Gordon David |
| Contributors | King, Valerie, Koop, Ben F. |
| Source Sets | University of Victoria |
| Language | English, English |
| Detected Language | English |
| Type | Thesis |
| Rights | Available to the World Wide Web |
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