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Please use this identifier to cite or link to this item: http://ntour.ntou.edu.tw:8080/ir/handle/987654321/27758

Title: An SSR Comparative Genomics Database and Its Applications
Authors: Tun-Wen Pai;Meng-Chang Hsiao;Chien-Ming Chen;Wen-Shyong Tzou;Ron-Shan Chen
Contributors: NTOU:Department of Computer Science and Engineering
Keywords: Simple sequence repeat;comparative genomics;conserved region;database
Date: 2008-03
Issue Date: 2011-10-21T02:33:55Z
Publisher: International Conference on Complex, Intelligent and Software Intensive Systems(CISIS 2008)
Abstract: Abstract:Simple sequence repeats (SSRs) play as important genetic markers in genome mapping projects and polymorphic research. In this study, we have designed a database which facilitates the searching and position verification of SSRs and provides comparative genomics information among various species. However, performing in silico analysis of biological data sometimes attempts to result in high false positive rates. In order to promote the specificity of discovered SSRs from the proposed system, we take advantage of evolutionarily conserved segments among sequences from various species. Users are able to choose specific species as targets to filter out SSRs which are not located in conserved regions. Screening processes narrow down candidate SSRs and improve the performance of specificity. In this database, there are eleven representative species collected for comparative genomics analysis. Taking the comparison between zebrafish and medaka fish as an example, 60,363 SSRs from zebrafish genome are found in conserved regions in which 6.20% SSRs are located in protein-coding regions, 0.20% in 5psilaUTR, 0.87% in 3psilaUTR, 51.26% in intron, and 41.45% in intergenic region. Each SSR is precisely allocated and annotated in this database for further applications.
Relation: pp.661-666
URI: http://ntour.ntou.edu.tw/handle/987654321/27758
Appears in Collections:[資訊工程學系] 演講及研討會

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