MiIP:单体鉴定和分离程序

Christopher Bun, William Ziccardi, J. Doering, C. Putonti
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引用次数: 2

摘要

基因组DNA中的重复元素在功能和进化上都具有信息性。从头开始发现这些序列在计算上具有挑战性,而且对这些重复序列的选择通常是宽松的;因此,重复元素之间的序列同一性可以显著变化。在这里,我们提出了一个新的应用程序,单体鉴定和分离程序(MilP),它提供了搜索特定重复以及在较大的基因组序列中发现重复元素的功能。为了比较MilP与其他重复序列检测工具的性能,我们对合成序列以及几个α21-II克隆和HC21 BAC序列进行了分析。MilP的主要优点是,它是一个单一的工具,既可以搜索已知的单基因序列,也可以根据用户要求的搜索灵敏度从头开始发现重复序列的发生。此外,报告功能有助于方便后续的系统发育分析。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
MiIP: The Monomer Identification and Isolation Program
Repetitive elements within genomic DNA are both functionally and evolutionarily informative. Discovering these sequences ab initio is computationally challenging, compounded by the fact that selection on these repeats is often relaxed; thus sequence identity between repetitive elements can vary significantly. Here we present a new application, the Monomer Identification and Isolation Program (MilP), which provides functionality to both search for a particular repeat as well as discover repetitive elements within a larger genomic sequence. To compare MilP's performance with other repeat detection tools, analysis was conducted for synthetic sequences as well as several α21-II clones and HC21 BAC sequences. The primary benefit of MilP is the fact that it is a single tool capable of searching for both known monomelic sequences as well as discovering the occurrence of repeats ab initio, per the user's required sensitivity of the search. Furthermore, the report functionality helps easily facilitate subsequent phylogenetic analysis.
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