| name | biosurfdb |
| description | BioSurfDB — curated portal for biosurfactant production and hydrocarbon biodegradation genes/pathways with BLAST and related metagenome analysis helpers. Use for surfactant/biodegradation-focused searches and pathway browsing. Portal: https://www.biosurfdb.org/. Route via dom-biosurfactant. Offline experimental gene sets → hadeg; glycan DOM → dbcan.
|
| license | MIT |
| category | analysis-tools |
| tags | ["BioSurfDB","biosurfactant","biodegradation","hydrocarbon","DOM","portal"] |
| upstream | https://www.biosurfdb.org/ |
| stage | mining |
BioSurfDB
Portal: https://www.biosurfdb.org/ ·
Tutorial: https://www.biosurfdb.org/tutorial.php (paths may change — verify)
Citation
Oliveira, J. S. et al. BioSurfDB: knowledge and algorithms to support
biosurfactants and biodegradation studies. Database 2015, bav033 (2015).
https://doi.org/10.1093/database/bav033
See also docs/references.md.
Analytical thinking
BioSurfDB integrates biosurfactant catalogues, biodegradation-relevant genes /
pathways, and metagenome-oriented BLAST utilities. Useful for
surfactant class exploration and HC biodegradation context. Large private
metagenome uploads may need admin/contact per portal policy — for fully local
pipelines prefer hadeg FASTA + DIAMOND.
MEGAN users sometimes map DIAMOND hits onto BioSurfDB classifications — cite
both MEGAN and BioSurfDB if used.
| vs | Prefer BioSurfDB when |
|---|
hadeg | Portal pathways / curated surfactant lists / interactive BLAST |
antismash | Pathway/DB hit tables vs BGC coordinates |
dbcan | Surfactant/HC focus vs carbohydrate DOM |
How to run
Decision tree
Biosurfactant / biodegradation portal need?
├─ Curated portal / pathway browse → biosurfdb
├─ Local experimental gene DB → hadeg
├─ Glycan DOM → dbcan
└─ BGC structure → antismash
Related skills
dom-biosurfactant · hadeg · dbcan · antismash · dram ·
microbial-mining · tool-selection
