| name | hh-suite |
| description | HH-suite3 (HHblits / HHsearch) — remote protein homology via HMM–HMM alignment (Söding lab). Use when: (1) Sequence identity is too low for BLAST/MMseqs easy hits, (2) Building/searching profile HMMs (BFD, UniClust, Pfam-style DBs), (3) Feeding sensitive MSAs into structure prediction Upstream: https://github.com/soedinglab/hh-suite. Route via homology-search; complements mmseqs2 and foldseek.
|
| license | MIT |
| category | analysis-tools |
| tags | ["HHblits","HHsearch","HH-suite","HMM","remote-homology","search"] |
| upstream | https://github.com/soedinglab/hh-suite |
| stage | function |
HH-suite3
Upstream: soedinglab/hh-suite
Citation
Remmert, M., Biegert, A., Hauser, A. & Söding, J. HHblits: lightning-fast
iterative protein sequence searching by HMM-HMM alignment. Nat. Methods
9, 173–175 (2012). https://doi.org/10.1038/nmeth.1818
See also docs/references.md.
Analytical thinking
Profile–profile search (HMM–HMM) recovers remote homologs that single-sequence
tools miss. Still a sequence/profile method — pair with foldseek when
structures exist. Large DBs (BFD via PLASS catalogues, UniClust) need disk and
careful pinning.
| vs | Prefer HH-suite when |
|---|
mmseqs2 | Need iterative profile search / MSA for folding |
foldseek | No structures yet; profile MSA / remote homology |
plmsearch | Classical HMM profiles preferred over PLM embeddings |
How to run
hhblits -i query.faa -o temp/hh/query.hhr -oa3m temp/hh/query.a3m \
-n 1 -d /path/to/hh_database
Decision tree
Remote homology without structure?
├─ Profile HMM iterative search → hh-suite (hhblits)
├─ Fast catalogue AA search → mmseqs2
├─ Structure / 3Di → foldseek
└─ Vector DB → erast
Related skills
homology-search · mmseqs2 · foldseek · plass · plmsearch ·
tool-selection
