isescan

name	isescan
description	ISEScan — automated annotation of insertion sequence (IS) elements in prokaryotic genomes via profile HMMs. Use for IS family catalogues on MAGs or contigs as part of MGE refinement beyond geNomad. Upstream: https://github.com/xiezhq/ISEScan. Route via microbial-mining; pair with mobileog / integronfinder.
license	MIT
category	analysis-tools
tags	["ISEScan","IS","insertion-sequence","MGE","genome-mining"]
upstream	https://github.com/xiezhq/ISEScan
stage	mining

ISEScan

Upstream: xiezhq/ISEScan

Citation

Xie, Z. & Tang, H. ISEScan: automated identification of insertion sequence elements in prokaryotic genomes. Bioinformatics 33, 3340–3347 (2017). https://doi.org/10.1093/bioinformatics/btx433

See also docs/references.md.

Analytical thinking

IS elements drive rearrangements and can flank ARGs/BGCs. ISEScan reports IS families/copies; it does not replace plasmid/virus classifiers (genomad) or integron detection (integronfinder).

How to run

# install per upstream; typical pattern
isescan.py genome.fna output_dir
# pin ISEScan + HMM library versions

Decision tree

Need IS annotation?
├─ Yes → isescan
├─ Broader MGE proteins → mobileog
├─ Integrons → integronfinder
└─ Plasmid/virus contigs → genomad

Related skills

mobileog · integronfinder · genomad · rgi · microbial-mining · tool-selection