| name | mobileog |
| description | mobileOG-db — manually curated protein families for bacterial MGE life-cycle functions (integration/excision, replication/recombination/repair, stability/defense, transfer, phage-related) with diamond + mobileOG-pl parsing. Use to annotate MGE machinery on MAG/contig proteins beyond geNomad contig scores. Upstream: https://github.com/clb21565/mobileOG-db. Portal: https://mobileogdb.flsi.cloud.vt.edu/. Route via microbial-mining.
|
| license | MIT |
| category | analysis-tools |
| tags | ["mobileOG","MGE","plasmid","phage","ICE","genome-mining"] |
| upstream | https://github.com/clb21565/mobileOG-db |
| stage | mining |
mobileOG-db
Upstream: clb21565/mobileOG-db ·
Portal: https://mobileogdb.flsi.cloud.vt.edu/
Citation
Brown, C. L. et al. mobileOG-db: a Manually Curated Database of Protein
Families Mediating the Life Cycle of Bacterial Mobile Genetic Elements.
Appl. Environ. Microbiol. 88, e00991-22 (2022).
https://doi.org/10.1128/aem.00991-22
See also docs/references.md.
Analytical thinking
mobileOG-db labels proteins into MGE machinery categories (IE, RRR, STD, T, P).
Use after gene call to interpret what MGE functions are present; pair with
genomad (contig-level plasmid/virus calls), isescan (IS), integronfinder
(integrons), and mob-suite (plasmid typing).
Hit ≠ complete conjugative element. Pin database release (e.g. beatrix) and
DIAMOND thresholds from upstream/mobileOG-pl docs.
How to run
diamond blastp -q proteins.faa --db mobileOG-db.dmnd -o hits.tsv \
--outfmt 6 …
Decision tree
MGE functional proteins?
├─ Contig plasmid/virus scores → genomad
├─ MGE protein machinery categories → mobileog
├─ Insertion sequences → isescan
├─ Integrons / cassettes → integronfinder
├─ Plasmid MOB/replicon typing → mob-suite
└─ ARG on MGEs → rgi ∩ genomad/mobileog context
Related skills
genomad · isescan · integronfinder · mob-suite · rgi · plasmaag ·
microbial-mining · tool-selection
