Discovering Functional Simple Sequence Repeat through Comparative Genomics

• Main Authors: Chien-Ming Chen, 陳建銘
• Other Authors: Tun-Wen Pai
• Format: Others
• Language: en_US
• Published: 2009
• Online Access: http://ndltd.ncl.edu.tw/handle/68588051617247352445

碩士 === 國立臺灣海洋大學 === 資訊工程學系 === 97 === Simple Sequence Repeats (SSRs) are sequences of repeated nucleotides in genomes consisting of a continuous repeated basic pattern from moninucleotide to hexanucleotide. SSRs are usually employed as genetic markers, but recent studies have shown that some SSRs played important roles in gene regulation and SSR disorder may cause different genetic diseases. Therefore, identifying functional SSRs becomes useful in various applications such as understanding genes regulation, screening genetic diseases, and breeding for economic species. However, due to abundant number of SSRs within each genome, it’s very difficult to identify functional SSRs from individual genome sequences. Hence, in this study, an efficient algorithm based on auto-correlation for discovering functional SSRs in-silico was proposed, and a genomic range SSR database for multiple model species was built as well. This database provides comparative genomics information including cross-species gene conserved regions and homologous genes for filtering putative functional SSRs. A degenerate primer design tool is also available to facilitate biologists for designing biological experiments. Furthermore, based on the cross species analysis of over representation of SSRs within different gene subsets annotated by Gene Ontology terms, we have observed the connection between the gene functions and several specific SSR patterns. Finally, the Online Mendelian Inheritance In Man (OMIM) database was also integrated with the core searching techniques for detecting unknown SSR regulators of genetic diseases.