rust-ise
========
Copyright (c) Sunju Kim.
Licensed under GPL-3.0-or-later (see LICENSE).
Third-party data sources used by `rust-ise build-db`
----------------------------------------------------
The `build-db` subcommand builds the union IS profile database and the FP-control
reference from third-party sequence data. `--fetch-sources` downloads that data,
at pinned commits, directly from its upstream origin onto the user's machine — this
crate does not redistribute it. Each source retains its own copyright and license,
and users of the built database should cite the sources below.
1. ISfinder sequences (IS.faa, IS.csv, IS.fna)
© the ISfinder team — ISfinder, https://isfinder.biotoul.fr
Fetched from the community mirror `thanhleviet/ISfinder-sequences`
(https://github.com/thanhleviet/ISfinder-sequences), pinned commit
bedbeb5c16618eca3e16ef74adf865d6b88cafb5.
Citation: Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M.
"ISfinder: the reference centre for bacterial insertion sequences."
Nucleic Acids Research 34 (2006) D32–D36. doi:10.1093/nar/gkj014
2. ISOSDB (ISOSDB.V3.fna.zip, IS_fam_annot.txt)
From `joshuakirsch/pseudoR` (https://github.com/joshuakirsch/pseudoR),
pinned commit 9e44803ddca7f2af678c72c9f02284e94a204164 (see that repo's LICENSE).
Citation: Kirsch JM, Hryckowian AJ, Duerkop BA.
"A metagenomics pipeline reveals insertion sequence-driven evolution of the
microbiota." Cell Host & Microbe 32 (2024). (pseudoR / ISOSDB)
3. Host-lineage negative pool (negharvest_reps.fna)
A curation artifact of this project (representative non-IS host CDS used as the
FP-control negative set), distributed as a GitHub Release asset of
github.com/necoli1822/rust-ise and pinned by sha256. Derived from public GTDB
representative genomes; see the release notes for provenance.
Bundled Rust dependencies retain their own licenses; see each crate for details.