| name | mebs |
| description | MEBS (Multigenomic Entropy-Based Score) — score genomes/metagenomes for biogeochemical cycle machinery via informative Pfam domains; strongest for sulfur (S), also supports N, O, CH4, and Fe cycle scores. Use for comparative cycle enrichment across large (meta)genome collections. Upstream: https://github.com/valdeanda/mebs (also eead-csic-compbio/metagenome_Pfam_score). Route via element-cycling. Gene-level Fe → fegenie; multi-element diagrams → metabolic.
|
| license | MIT |
| category | analysis-tools |
| tags | ["MEBS","sulfur","S","N","CH4","Fe","biogeochemistry","element-cycling"] |
| upstream | https://github.com/valdeanda/mebs |
| stage | mining |
MEBS
Upstream: valdeanda/mebs ·
legacy/core: https://github.com/eead-csic-compbio/metagenome_Pfam_score
Citation
De Anda, V. et al. MEBS, a software platform to evaluate large (meta)genomic
collections according to their metabolic machinery: unraveling the sulfur cycle.
Gigascience 6, 1–17 (2017).
https://doi.org/10.1093/gigascience/gix096
See also docs/references.md.
Analytical thinking
MEBS compresses curated cycle machinery into relative-entropy scores over
Pfam domains. Benchmarked deeply on the sulfur (S) cycle; documentation
also supports N, O, CH₄, and Fe scoring modes. Ideal for
ranking many genomes/metagenomes by cycle “machinery presence,” not for
drawing full METABOLIC-style pathway cartoons.
| vs | Prefer MEBS when |
|---|
metabolic | Comparative S/N/CH₄/Fe scores across large collections |
fegenie | Score-level Fe vs explicit Fe gene neighborhoods |
dram | Cycle enrichment metric vs distilled product tables |
Input: directory of .faa peptide FASTA; use genomic vs metagenomic mode per
docs (fragmentary metagenomes need the metagenomic entropy tables).
How to run
Decision tree
Cycle scoring need?
├─ S (or N/O/CH₄/Fe) entropy scores → mebs
├─ C/N/S diagrams + networks → metabolic
├─ Fe gene calls → fegenie
└─ Broad distillate → dram
Related skills
element-cycling · metabolic · fegenie · dram · microbial-mining ·
tool-selection
