| 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
isescan.py genome.fna output_dir
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
