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Fig. 1 | Mobile DNA

Fig. 1

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

Fig. 1

The work-flow of Genome ARTIST describing the main steps conducting to the detection of TGN as the transposon’s insertion site. Overlapped decamers (or BIs) are used for hashing the genomic and transposon reference sequences, but also for the interrogation of the query sequence against the hash table, in order to detect BIs associated with the reference. The matching BIs are merged if they are adjacent or overlapped, then the resulting contiguous association intervals are extended to EIs (the SW1 step). The adjacent and overlapping EIs are merged to MEIs, which are rigorously aligned against the reference sequences during the SW2 step to map partial alignments as TPAs and GPAs. Each partial alignment contains a nucleus, a sub-alignment which is critical during the merging step. The specific joining algorithm of Genome ARTIST, which includes a SW3 step, prioritizes the nucleus of TPA but also searches for the best possible TGN whenever small-scale mutations or sequencing artifacts are present close to the joining border

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