iMapper - Insertional Mutagenesis Mapper

iMapper is a sequence analysis tool designed specifically for large-scale analysis of insertional mutagenesis tag sequences against vertebrate and invertebrate genomes. It trims real genomic segments from linker-based PCR sequence input and automatically maps insertion sites onto an assembled genome. Learn more

Submissions are limited to 10000 sequences.

Download a file of 96 PiggyBac traces for test use.

Comments & Questions:

Citing iMapper
If you use iMapper to analyze your insertional datasets and find it useful, we would be appreciate if you could consider citing the reference that describes this work:

  • iMapper: a web application for the automated analysis and mapping of insertional mutagenesis sequence data against Ensembl genomes.

    Kong J, Zhu F, Stalker J and Adams DJ

    Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambs CB101HH, UK.

    Summary: 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 file 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.

    Availability: iMapper is web based and can be accessed at

    Funded by: Cancer Research UK: C20510/A6997; Wellcome Trust: 76943

    Bioinformatics (Oxford, England) 2008;24;24;2923-5

Submit your sequence to iMapper

Sequencing from:
Output option: Output all sequences
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Mutagen tag sequence:

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