鉴定奥利亚罗非鱼基因组中的重复元件：罗非鱼重复屏蔽软件。
Identification of repetitive elements in the genome of Oreochromis niloticus: tilapia repeat masker.
机构信息
Agricultural Research Organization, Institute of Animal Science, Bet Dagan, 50250, Israel.
出版信息
Mar Biotechnol (NY). 2010 Apr;12(2):121-5. doi: 10.1007/s10126-009-9236-8. Epub 2009 Nov 21.
Abstract
The large-scale bacterial artificial chromosome-end sequencing project of Nile tilapia (Oreochromis niloticus) has generated extensive sequence data that allowed the examination of the repeat content in this fish genome and building of a repeat library specific for this species. This library was established based on Tilapiini repeat sequences from GenBank, sequences orthologous to the repeat library of zebrafish in Repbase, and novel repeats detected by genome analysis using MIRA assembler. We estimate that repeats constitute about 14% of the tilapia genome and also give estimates for the occurrence of the different repeats based on the Basic Local Alignment Search Tool searches within the database of known tilapia sequences. The frequent occurrence of novel repeats in the tilapia genome indicates the importance of using the species-specific repeat masker prior to sequence analyses. A web tool based on the RepeatMasker software was designed to assist tilapia genomics.
摘要
尼罗罗非鱼（Oreochromis niloticus）的大规模细菌人工染色体末端测序项目产生了广泛的序列数据，这些数据允许我们检查这种鱼类基因组中的重复含量，并构建针对该物种的重复文库。这个文库是基于 GenBank 中的 Tilapiini 重复序列、Repbase 中与斑马鱼重复文库同源的序列以及通过使用 MIRA 组装器进行基因组分析检测到的新重复序列建立的。我们估计重复序列约占罗非鱼基因组的 14%，并根据在已知罗非鱼序列数据库中使用基本局部比对搜索工具进行的搜索，给出了不同重复序列出现的估计值。罗非鱼基因组中频繁出现新的重复序列表明，在进行序列分析之前，使用物种特异性的重复屏蔽工具非常重要。我们设计了一个基于 RepeatMasker 软件的网络工具，以协助罗非鱼基因组学研究。
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