The development of next-generation sequencing technology enables us to obtain a vast number of short reads from metagenomic samples. In metagenomic samples, the reads from different species are mixed together. So, metagenomic binning has been introduced to cluster reads from the same or closely related species and metagenomic annotation is introduced to predict the taxonomic information of each read. Both metagenomic binning and annotation are critical steps in downstream analysis. This thesis discusses the difficulties of these two computational problems and proposes two algorithmic methods, MetaCluster 5.0 and MetaAnnotator, as solutions. There are six major challenges in metagenomic binning: (1) the lack of reference genomes; (2) uneven abundance ratios; (3) short read lengths; (4) a large number of species; (5) the existence of species with extremely-low-abundance; and (6) recovering low-abundance species. To solve these problems, I propose a two-round binning method, MetaCluster 5.0. The improvement achieved by MetaCluster 5.0 is based on three major observations. First, the short q-mer (length-q substring of the sequence with q = 4, 5) frequency distributions of individual sufficiently long fragments sampled from the same genome are more similar than those sampled from different genomes. Second, sufficiently long w-mers (length-w substring of the sequence with w ≈ 30) are usually unique in each individual genome. Third, the k-mer (length-k substring of the sequence with k ≈ 16) frequencies from reads of a species are usually linearly proportional to that of the species’ abundance. The metagenomic annotation methods in the literatures often suffer from five major drawbacks: (1) unable to annotate many reads; (2) less precise annotation for reads and more incorrect annotation for contigs; (3) unable to deal with novel clades with limited references genomes well; (4) performance affected by variable genome sequence similarities between different clades; and (5) high time complexity. In this thesis, a novel tool, MetaAnnotator, is proposed to tackle these problems. There are four major contributions of MetaAnnotator. Firstly, instead of annotating reads/contigs independently, a cluster of reads/contigs are annotated as a whole. Secondly, multiple reference databases are integrated. Thirdly, for each individual clade, quadratic discriminant analysis is applied to capture the similarities between reference sequences in the clade. Fourthly, instead of using alignment tools, MetaAnnotator perform annotation using k-mer exact match which is more efficient. Experiments on both simulated datasets and real datasets show that MetaCluster 5.0 and MetaAnnotator outperform existing tools with higher accuracy as well as less time and space cost. / published_or_final_version / Computer Science / Doctoral / Doctor of Philosophy

published_or_final_version / Medical Sciences / Master / Master of Medical Sciences

published_or_final_version / Zoology / Master / Master of Philosophy

No description available.

Nucleotide sequence data from several pea (Piswn sativum L.) seed storage protein genes was obtained. Of two legumin genes sequenced, one was shown to be a pseudogene, apparently once coding for a polypeptide belonging to the 'major' legumin class, whilst the other was shown to be a functional gene coding for a polypeptide of the 'minor' legumin class. Sequence data was also obtained for two vicilin genes. Complete sequencing of one revealed it to be truncated by sequence of unknown origin at its 3' end, whilst partial sequence for the other suggested the presence of a stop codon in the coding region. These findings implied that both vicilin genes are no longer functional. Additionally, various comparisons of nucleic acid and amino acid sequence data were made between these genes and also with other legume seed storage protein genes. Results showed these genes conform with the major structural features of eukaryotic genes, and also revealed the presence of potential tissue -specific regulatory elements in the 5' flanking regions of the genes. Dendrograms for legume 11S and 7S classes of globulin seed storage protein genes clearly supported the model theory of each class having arisen by successive duplications from a common ancestral gene.

Thesis (PhD)--University of South Australia, 2003.

Thesis (Ph. D.)--University of Adelaide, Dept. of Biochemistry, 1985. / Includes bibliographical references (leaves [127-137]).

Thesis (Ph. D.)--University of Adelaide, Dept. of Biochemistry, 1986. / Includes bibliographical references (leaves 147-165).

Thesis (M.Phil.)--Hong Kong University of Science and Technology, 2007. / Includes bibliographical references (leaves 89-93). Also available in electronic version.

Thesis (Ph. D.)--University of Texas at Austin, 2007. / Vita. Includes bibliographical references.