sokrypton/afdb-msa-index

AlphaFold DB minimizer index

A static sequence-search index over 239,602,633 AlphaFold DB v6 entries (99.4% of the database), designed to be queried directly from a browser with HTTP Range requests. No server, no search engine, no MMseqs2.

It exists to answer one question quickly: which AFDB entry is ≥90% identical to my sequence? — so that entry's precomputed MSA can be borrowed and re-indexed onto the query instead of computing a new alignment.

Used by AFDB MSA.

Cost of a query

~45 ranged requests, ~50 KB, ~1 ms  — independent of index size

Twelve minimizer seeds per query; each costs an 8-byte read of buckets.u32 (a prefix-sum array, so slots b and b+1 arrive together) and one read of its posting list.

Layout

file	size	contents
meta.json	2 KB	entry count, k, target seeds, bucket bits, file table
buckets.u32	134 MB	2^25+1 prefix offsets: a seed's high bits give its posting range
post-000..009.bin	14.2 GB	5 bytes per posting: 1-byte key residual + 4-byte entry id
acc.bin	2.88 GB	fixed 12-byte accessions, so an entry id is its byte offset

Seeds are 31-bit. The top 25 bits address a bucket; the stored 1-byte residual is the seed's low 8 bits, overlapping the bucket by 2 — a harmless redundancy that still pins down the 6 low bits the bucket does not carry. Residual collisions are filtered by the alignment that follows, since shared-seed count is a prefilter.

Parameters

k = 10          10-mers; survive 90% identity with p = 0.9^10 = 0.35
target = 12     seeds per sequence, so P(share >=1) = 1 - 0.65^12 = 99.2%
w adaptive      window = len/12, clamped to [4,128]

The window adapts to length rather than being fixed: a fixed window undersamples short proteins — at k=12 w=16 a 142-residue globin got 8 seeds and shared none with a real 90% relative on two of three tries.

Measured against BLAST

16 AFDB sequences with 5% of positions mutated, versus BLAST on full UniProtKB:

	index	BLAST
hits at ≥90% identity	100%	81%
median identity	95%	95%
time	1 ms	287 s

The index also wins outright on some queries (94% vs 41% on one). That is the corpus, not cleverness: 63% of AFDB entries have been deleted from current UniProtKB, so BLAST cannot return them and settles for a distant relative. AFDB is its own authority here.

Limits

• Sensitivity fades below ~70% identity. Exact-k-mer seeding is reliable above ~90% and degrades below. That is deliberate — the target is close relatives worth borrowing an MSA from.
• Repetitive and low-complexity sequence yields few distinct seeds (a homopolymer collapses to one), so such queries retrieve weakly. A thin candidate list is not evidence that nothing similar exists.
• Entries only, not sequences. The index maps seeds to AFDB accessions; the residues come from AlphaFold DB's own API. Note that most AFDB accessions no longer resolve in current UniProtKB.

Building

From sequences.fasta (118 GB) with the tools in the repo:

for i in $(seq 0 23); do
  node tools/afdb-shard.mjs part_$(printf '%02d' $i).fa shards/ $i &
done; wait
node --max-old-space-size=120000 tools/afdb-merge.mjs shards/ index/

About 5 minutes of sharding on 24 cores, 2.5 minutes to merge.

Attribution

Derived from the AlphaFold Protein Structure Database (EMBL-EBI / Google DeepMind), release v6, which is distributed under CC-BY-4.0. This index inherits that licence.

Varadi et al. AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Research (2022).