Genome ARTIST: a robust, high-accuracy aligner tool for mapping transposon insertions and self-insertions

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Accurate mapping of artificial transposon (AT) insertions is crucial for mutagenesis studies in model organisms.
• Challenges include sequencing artifacts, single nucleotide polymorphisms (SNPs), and small insertions near transposon inverted repeats (TIRs).
• Mapping transposon self-insertions is particularly difficult, with no dedicated tools available.

Purpose of the Study:

• To develop a robust tool for accurate nucleotide-level mapping of AT insertions and self-insertions.
• To address limitations of existing methods in handling sequencing artifacts and complex insertion events.

Main Methods:

• Developed Genome ARTIST, a pairwise gapped aligner for small to medium-scale mutagenesis experiments.
• Employs a heuristic approach and a multi-step Smith-Waterman adapted algorithm for DNA sequence similarity and alignment.
• Integrates with Ensembl and GenBank genomes, and specifically utilizes FlyBase annotation data for Drosophila melanogaster.

Main Results:

• Genome ARTIST accurately maps AT insertions and self-insertions, overcoming common mapping errors.
• Demonstrated robustness compared to other alignment tools using real and simulated data from Drosophila melanogaster and Mus musculus.
• Provides a user-friendly interface detailing the genomic landscape around insertions.

Conclusions:

• Genome ARTIST is a user-friendly, stand-alone application for high-accuracy transposon insertion mapping.
• The tool also supports routine alignments, SNP detection, and primer/probe specificity checks.
• Genome ARTIST is open-source software available for download.