iMapper: a web application for the automated analysis and mapping of insertional mutagenesis sequence data against Ensembl genomes
iMapper: a web application for the automated analysis and mapping of insertional mutagenesis sequence data against Ensembl genomes
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DOI：
10.1093/bioinformatics/btn541
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发表时间：
2008-12-15
期刊：
影响因子：
5.8
通讯作者：
Adams, David J.
中科院分区：
文献类型：
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作者：
Kong, Jun;Zhu, Fei;Adams, David J.
插入突变是基因发现的有力手段。为了鉴定插入位点在基因组中的位置，可以采用基于接头的聚合酶链式反应（PCR）方法（例如splinkerette-PCR）。我们开发了一个名为iMapper（插入突变作图和分析工具）的网络应用程序，用于有效分析脊椎动物和无脊椎动物Ensembl基因组的插入位点序列读数。将基于接头的序列作为输入，iMapper扫描并修剪序列以去除接头和源自插入诱变剂的序列。然后，该软件鉴定并去除来源于嵌合基因组片段、载体或转座子多联体的污染序列，然后将剪切的序列读数呈现给序列映射服务器，该服务器将它们与Ensembl基因组进行比对。然后可以在基因组特征（例如基因结构）的背景下在Ensembl中导航插入位点。iMapper还生成基于测试的核酸或蛋白质序列格式（FASTA）和通用格式。Ie格式（GFF）文件，并提供针对核型的映射插入位点的图形概述。iMapper专为高通量应用而设计，可以有效地处理数千个DNA序列读数。
Insertional mutagenesis is a powerful method for gene discovery. To identify the location of insertion sites in the genome linker based polymerase chain reaction (PCR) methods (such as splinkerette-PCR) may be employed. We have developed a web application called iMapper (Insertional Mutagenesis Mapping and Analysis Tool) for the efficient analysis of insertion site sequence reads against vertebrate and invertebrate Ensembl genomes. Taking linker based sequences as input, iMapper scans and trims the sequence to remove the linker and sequences derived from the insertional mutagen. The software then identifies and removes contaminating sequences derived from chimeric genomic fragments, vector or the transposon concatamer and then presents the clipped sequence reads to a sequence mapping server which aligns them to an Ensembl genome. Insertion sites can then be navigated in Ensembl in the context of genomic features such as gene structures. iMapper also generates test-based format for nucleic acid or protein sequences (FASTA) and generic. le format (GFF) files of the clipped sequence reads and provides a graphical overview of the mapped insertion sites against a karyotype. iMapper is designed for high-throughput applications and can efficiently process thousands of DNA sequence reads.