Data coverage
A collection of prebuilt protein sequence databases for multiple sequence alignment (MSA) search. MSAs are the main input of protein structure prediction and are also used to study conservation, coevolution and protein function. The nine databases, in the native formats of MMseqs2 and HH-suite, derive from UniProt UniRef100 (release 202601), the reduced BFD, MGnify (release 202404), EnVhogDB and the Logan protein catalogue from the NCBI Sequence Read Archive. The sequences of UniRef100, MGnify and the reduced BFD were re-clustered, EnVhogDB was re-clustered at its upstream standard level, and Logan was built into an MMseqs2 expandable-profile database. Each database is published as one .tar.zst archive. They are set up for Thal-Kak, a pipeline that unifies several structure prediction models, so that its local MSA search writes MSAs in the input format of those models.
Access & permitted use
Review the publisher’s documentation for availability, eligibility and permitted uses, including commercial analysis, model training and redistribution.
Each database carries the license of the source it derives from; no database mixes sources. LICENSE.txt at the bucket root is the full record of upstream licenses, attribution, citation and changes. | Archives | License | Source | | --- | --- | --- | | hhblits/uniref100202601 | CC BY 4.0 | UniProt UniRef100, release 202601 | | mmseqs/bfdreduced | CC BY-SA 4.0 | BFD reduced subset, via the AlphaFold databases | | mmseqs/mgnifyclusters, hhblits/mgnifyclusters | CC0 1.0 | MGnify protein database, release 202404 | | mmseqs/envhogstd, hhblits/envhog | CC BY 4.0 | EnVhogDB | | mmseqs/loganhuman, hhblits/loganhuman, hhblits/logannonhuman | No license is granted. NCBI Policy and NIH Genomic Data Sharing Policy | Logan v1 (SRA cutoff 2023-12-10) |
Need help sourcing data?
Tell us your required fields, population, geography and time period. We can review suitable sources and licensing options.
Request sourcing help