textWith the advent of whole genome sequencing, we now have an abundance of whole
genomes which have been sequenced and we have entered an era when algorithms
can address problems at the whole genome level. In the past, sequencing efforts
often focused on a single gene, and therefore, existing algorithms are at the scale
of a single gene. With whole genome sequencing, we have access to sequence data
for the entire genome of an organism or an organelle and algorithms are needed
for whole genome analysis. In this research, we have addressed new computational
problems that have arisen out of the availability and abundance of whole genome
data.
In genome annotation, all of the genes of a genome are located and identified
in preparation for publication of the complete genome sequence. We address the
problem of genome annotation with a software package that allows researchers to
locate and identify all the genes in a genome and prepare the genome for direct
submission to GenBank. A difficult problem that arises in the annotation of organellar
genomes is the identification of animal mitochondrial transfer RNA genes.
We present an experimental evaluation a set of methods (including our own) for
identifying tRNAs.
The problem of reconstructing phylogenies from gene order data involves
recreating the evolutionary history of a set of organisms based on the order and
direction of the genes in the genomes. This can give insight into mechanisms of
large-scale evolutionary events. We present a new method for gene order phylogeny
reconstruction, as well as improvements to an existing method, and evaluate the
results on both real and simulated datasets.
Finally, we address the problem of identification of regulatory elements. Understanding
gene expression is one of the most pressing unsolved problems in molecular
biology today because gene expression controls all of the metabolic and developmental
processes in an organism. We present a new method which uses a
comparative genomics approach which is made possible now that we have access to
the complete DNA sequences of many sets of related organisms.Computer Science