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    Please use this identifier to cite or link to this item: http://asiair.asia.edu.tw/ir/handle/310904400/26236


    Title: 基因群組搜尋演算法之研究
    Authors: 呂威甫
    Contributors: 資訊學院;資訊工程學系
    Keywords: 比較基因體學;基因重組;基因群組;近似共同區間
    Date: 2011
    Issue Date: 2013-07-18 15:52:17 (UTC+8)
    Abstract: 基因重組造成物種間基因順序的改變,兩個親源接近的原核生物,通常會有許多基因 內容相同但順序的不同的染色體片段,稱為基因群組。基因群組中的基因有某著種程 度的功能相關性,使得這群基因在親源關係相近的物種中仍會保持相鄰的關係,只是 其前後順序會有所不同。基因群組在演化樹的建構與基因功能的預測都扮演了重要的 角色,是比較基因體學的研究中一個重要的問題。本計畫將討論基因群組搜尋問題並 發展相關的軟體工具。我們將由近似共同區間的角度探討基因群組的搜尋問題,其中 基因體將以字串表示,而字串間的近似共同區間則定義為基因群組。初步我們改進我 們的O(n 3)近似共同區間的演算法。接下來,我們將進一步討論集合轉換距離或其他定 義近似共同區間的方式。同時,我們將運用所發展出來的演算法建構基因群組搜尋軟 體工具,並進行實際生物資料的比對,我們有興趣的是尋找水稻與阿拉伯芥以及禾本 科植物之間的基因群組。

    Genome rearrangements reorganize the gene order in the chromosome. Usually two closely related prokaryotes share many gene clusters, which are sets of genes in close proximity to each other, but not necessarily contiguous nor in the same order in both genomes. Genes in gene clusters are functional related such that the cluster of genes in closely related organisms will appear continuously but in different order. It plays an important role in the construction of phylogenetic trees and prediction of gene functions. Thus, finding gene clusters is an important problem in comparative genomics. In this project, we will discuss gene clusters finding problem and develop its software tools. We will use the model of approximate common intervals, that is, genomes are considered as strings and gene clusters are defined as approximate common intervals in strings. At first, we will improve our O(n3) algorithm for finding approximate common intervals with set symmetric < k. And then, we will consider other definitions of approximate common intervals, such as set transformation distance. In the meanwhile, we will construct the gene finding software, and test our algorithms using real biology data. We are interesting in finding gene clusters among rice, arabidopsis and grass genomes.
    Appears in Collections:[資訊工程學系] 科技部研究計畫

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