{
"page": "coverage.html",
"title": "Coverage",
"source": {
"repo": "seanome/2024-kmerseek-analysis",
"commit": "4a4b11714ddb740f8a7e324058b26bee8fb35af4",
"commit_date": "2026-10-15T13:12:56Z",
"path": "results/leaderboard",
"copied_at": "2026-10-15T13:44:05Z",
"sha256": {
"results.parquet": "0c0cf94b5fc40587cab2ffbf7aaf84df9b5475037cc0d818ad2f452a9c73a837",
"compute.parquet": "8a47ba2123c60cbb41b4833c9f96661934369137b72c5d81ef0808c98247e435",
"coverage.md": "c10b26730d8dc44b16120bd2f6ee87eb8ed0db3efa40398b339ddac0b0cb7781",
"provenance.json": "22e54f206354e42208f8a78c4f4827f980ac1db2ce13153f2b077274552e4141",
"inventory.md": "8dc7040a38cf06af126bd08211edf1f6055c69fe9ac2b4088c6ba8f7f90e6c71",
"pileup/regions.parquet": "e97701d2fcb601babe25c7d5c6c82760ea19e460e9bc1d555fe5f8f69cb4d6d8",
"pileup/calls.parquet": "41bc1f6db7bf54f00370b11db2ffed61031d90a42895aa1697be26fc449ea958",
"pileup/provenance.json": "5ed6e70dd9e82b5200f089b9da3afc62d0a10cc6a51da86715f5f26d3aac9b9e"
},
"pileup_commit": "39d81ec90815cacbf3744199d1fa8e99ab28c6f4"
},
"text": [
{
"tag": "h1",
"text": "Coverage"
},
{
"tag": "p",
"text": "What has been measured, across every experiment in the tables, and what has not. Every × is a run still to do."
},
{
"tag": "p",
"text": "Data from 15 Oct 2026, commit 4a4b1171 (source)"
},
{
"tag": "figcaption",
"text": "Table 2a. Tool by subset of the proteins. The number under each filled square is the count of true instances scored, summed over experiments, query sets, relatives and truth sets. Hover a column name for its id in the tables."
},
{
"tag": "th",
"text": "Tool"
},
{
"tag": "th",
"text": "whole set, per relative"
},
{
"tag": "th",
"text": "% identity to nearest relative"
},
{
"tag": "th",
"text": "AlphaFold pLDDT"
},
{
"tag": "th",
"text": "Swiss-Prot feature type"
},
{
"tag": "th",
"text": "region length"
},
{
"tag": "td",
"text": "phmmer"
},
{
"tag": "td",
"text": "1,329,895"
},
{
"tag": "td",
"text": "952,047"
},
{
"tag": "td",
"text": "276,686"
},
{
"tag": "td",
"text": "181,647"
},
{
"tag": "td",
"text": "1,133,694"
},
{
"tag": "td",
"text": "MMseqs2"
},
{
"tag": "td",
"text": "1,158,512"
},
{
"tag": "td",
"text": "952,047"
},
{
"tag": "td",
"text": "276,686"
},
{
"tag": "td",
"text": "181,647"
},
{
"tag": "td",
"text": "1,133,694"
},
{
"tag": "td",
"text": "jackhmmer"
},
{
"tag": "td",
"text": "1,329,803"
},
{
"tag": "td",
"text": "952,047"
},
{
"tag": "td",
"text": "276,686"
},
{
"tag": "td",
"text": "181,647"
},
{
"tag": "td",
"text": "1,133,694"
},
{
"tag": "td",
"text": "MMseqs2, three rounds"
},
{
"tag": "td",
"text": "1,158,512"
},
{
"tag": "td",
"text": "952,047"
},
{
"tag": "td",
"text": "276,686"
},
{
"tag": "td",
"text": "181,647"
},
{
"tag": "td",
"text": "1,133,694"
},
{
"tag": "td",
"text": "HH-suite (hhsearch)"
},
{
"tag": "td",
"text": "1,158,512"
},
{
"tag": "td",
"text": "952,047"
},
{
"tag": "td",
"text": "276,686"
},
{
"tag": "td",
"text": "181,647"
},
{
"tag": "td",
"text": "1,133,694"
},
{
"tag": "td",
"text": "Foldseek"
},
{
"tag": "td",
"text": "1,110,504"
},
{
"tag": "td",
"text": "939,872"
},
{
"tag": "td",
"text": "231,206"
},
{
"tag": "td",
"text": "145,722"
},
{
"tag": "td",
"text": "1,085,594"
},
{
"tag": "td",
"text": "ProstT5 + Foldseek"
},
{
"tag": "td",
"text": "1,158,512"
},
{
"tag": "td",
"text": "952,047"
},
{
"tag": "td",
"text": "276,686"
},
{
"tag": "td",
"text": "181,647"
},
{
"tag": "td",
"text": "1,133,694"
},
{
"tag": "td",
"text": "kmerseek"
},
{
"tag": "td",
"text": "1,584,821"
},
{
"tag": "td",
"text": "1,105,115"
},
{
"tag": "td",
"text": "276,686"
},
{
"tag": "td",
"text": "181,647"
},
{
"tag": "td",
"text": "1,133,694"
},
{
"tag": "td",
"text": "hmmscan with Pfam"
},
{
"tag": "td",
"text": "8,793"
},
{
"tag": "td",
"text": "–"
},
{
"tag": "td",
"text": "8,234"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "8,793"
},
{
"tag": "td",
"text": "Folddisco (no card)"
},
{
"tag": "td",
"text": "590,559"
},
{
"tag": "td",
"text": "516,687"
},
{
"tag": "td",
"text": "121,049"
},
{
"tag": "td",
"text": "73,872"
},
{
"tag": "td",
"text": "590,559"
},
{
"tag": "td",
"text": "MMseqs2, search mode not recorded (no card)"
},
{
"tag": "td",
"text": "171,383"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "Reseek (no card)"
},
{
"tag": "td",
"text": "615,377"
},
{
"tag": "td",
"text": "516,687"
},
{
"tag": "td",
"text": "121,049"
},
{
"tag": "td",
"text": "73,872"
},
{
"tag": "td",
"text": "590,559"
},
{
"tag": "figcaption",
"text": "Table 2b. Tool by experiment. The number under each filled square is the count of true instances scored, summed over the query sets, relatives, truth sets and subsets of that experiment. Hover a column name for its id in the tables."
},
{
"tag": "th",
"text": "Tool"
},
{
"tag": "th",
"text": "Alphabets ranked on three test proteins (notebook 241)"
},
{
"tag": "th",
"text": "Invertebrate dark set: accuracy of the best kmerseek setting"
},
{
"tag": "th",
"text": "Invertebrate dark set: what kmerseek reaches"
},
{
"tag": "th",
"text": "Invertebrate dark set: Fmax against Pfam (notebook 291)"
},
{
"tag": "th",
"text": "Deep-twilight controls, 16 proteins (notebook 252)"
},
{
"tag": "th",
"text": "Short linear motifs (ELM) covered (notebook 253)"
},
{
"tag": "th",
"text": "Domain finding, 9 relatives"
},
{
"tag": "th",
"text": "Domain finding, 15 relatives (this leaderboard)"
},
{
"tag": "th",
"text": "Domain finding, test set of 2 relatives"
},
{
"tag": "th",
"text": "SCOPe40 structural classes, kmerseek 0.4 (notebook 277)"
},
{
"tag": "th",
"text": "SCOPe40, kmerseek 0.4, k below the usual minimum"
},
{
"tag": "th",
"text": "SCOPe40 control: alphabet letters shuffled"
},
{
"tag": "td",
"text": "phmmer"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "159,304"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "11,987"
},
{
"tag": "td",
"text": "92"
},
{
"tag": "td",
"text": "24,818"
},
{
"tag": "td",
"text": "1,547,820"
},
{
"tag": "td",
"text": "1,785,042"
},
{
"tag": "td",
"text": "344,906"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "–"
},
{
"tag": "td",
"text": "MMseqs2"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "24,818"
},
{
"tag": "td",
"text": "1,547,820"
},
{
"tag": "td",
"text": "1,785,042"
},
{
"tag": "td",
"text": "344,906"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "–"
},
{
"tag": "td",
"text": "jackhmmer"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "159,304"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "11,987"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "24,818"
},
{
"tag": "td",
"text": "1,547,820"
},
{
"tag": "td",
"text": "1,785,042"
},
{
"tag": "td",
"text": "344,906"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "–"
},
{
"tag": "td",
"text": "MMseqs2, three rounds"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "24,818"
},
{
"tag": "td",
"text": "1,547,820"
},
{
"tag": "td",
"text": "1,785,042"
},
{
"tag": "td",
"text": "344,906"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "–"
},
{
"tag": "td",
"text": "HH-suite (hhsearch)"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "24,818"
},
{
"tag": "td",
"text": "1,547,820"
},
{
"tag": "td",
"text": "1,785,042"
},
{
"tag": "td",
"text": "344,906"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "–"
},
{
"tag": "td",
"text": "Foldseek"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "92"
},
{
"tag": "td",
"text": "24,818"
},
{
"tag": "td",
"text": "1,547,820"
},
{
"tag": "td",
"text": "1,595,262"
},
{
"tag": "td",
"text": "344,906"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "–"
},
{
"tag": "td",
"text": "ProstT5 + Foldseek"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "24,818"
},
{
"tag": "td",
"text": "1,547,820"
},
{
"tag": "td",
"text": "1,785,042"
},
{
"tag": "td",
"text": "344,906"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "–"
},
{
"tag": "td",
"text": "kmerseek"
},
{
"tag": "td",
"text": "2"
},
{
"tag": "td",
"text": "159,304"
},
{
"tag": "td",
"text": "93,098"
},
{
"tag": "td",
"text": "11,987"
},
{
"tag": "td",
"text": "92"
},
{
"tag": "td",
"text": "24,818"
},
{
"tag": "td",
"text": "1,547,820"
},
{
"tag": "td",
"text": "1,785,042"
},
{
"tag": "td",
"text": "344,906"
},
{
"tag": "td",
"text": "44,970"
},
{
"tag": "td",
"text": "147,070"
},
{
"tag": "td",
"text": "122,854"
},
{
"tag": "td",
"text": "hmmscan with Pfam"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "6,998"
},
{
"tag": "td",
"text": "7,203"
},
{
"tag": "td",
"text": "11,619"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "–"
},
{
"tag": "td",
"text": "Folddisco (no card)"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "1,547,820"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "344,906"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "–"
},
{
"tag": "td",
"text": "MMseqs2, search mode not recorded (no card)"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "159,304"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "11,987"
},
{
"tag": "td",
"text": "92"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "–"
},
{
"tag": "td",
"text": "Reseek (no card)"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "24,818"
},
{
"tag": "td",
"text": "1,547,820"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "344,906"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "×"
},
{
"tag": "td",
"text": "–"
},
{
"tag": "p",
"text": "111 squares are filled, 81 are not run and 12 do not apply. Where each experiment's output came from, and which outputs were left out and why: inventory.md (copied with the tables)."
},
{
"tag": "h2",
"text": "What to run next"
},
{
"tag": "p",
"text": "One line per experiment: the tools it has not run yet."
},
{
"tag": "li",
"text": "Alphabets ranked on three test proteins (notebook 241): phmmer, MMseqs2, jackhmmer, MMseqs2, three rounds, HH-suite (hhsearch), Foldseek, ProstT5 + Foldseek, hmmscan with Pfam, Folddisco, MMseqs2, search mode not recorded, Reseek"
},
{
"tag": "li",
"text": "Invertebrate dark set: what kmerseek reaches: phmmer, MMseqs2, jackhmmer, MMseqs2, three rounds, HH-suite (hhsearch), Foldseek, ProstT5 + Foldseek, hmmscan with Pfam, Folddisco, MMseqs2, search mode not recorded, Reseek"
},
{
"tag": "li",
"text": "SCOPe40 structural classes, kmerseek 0.4 (notebook 277): phmmer, MMseqs2, jackhmmer, MMseqs2, three rounds, HH-suite (hhsearch), Foldseek, ProstT5 + Foldseek, hmmscan with Pfam, Folddisco, MMseqs2, search mode not recorded, Reseek"
},
{
"tag": "li",
"text": "SCOPe40, kmerseek 0.4, k below the usual minimum: phmmer, MMseqs2, jackhmmer, MMseqs2, three rounds, HH-suite (hhsearch), Foldseek, ProstT5 + Foldseek, hmmscan with Pfam, Folddisco, MMseqs2, search mode not recorded, Reseek"
},
{
"tag": "li",
"text": "Invertebrate dark set: accuracy of the best kmerseek setting: MMseqs2, MMseqs2, three rounds, HH-suite (hhsearch), Foldseek, ProstT5 + Foldseek, hmmscan with Pfam, Folddisco, Reseek"
},
{
"tag": "li",
"text": "Invertebrate dark set: Fmax against Pfam (notebook 291): MMseqs2, MMseqs2, three rounds, HH-suite (hhsearch), Foldseek, ProstT5 + Foldseek, hmmscan with Pfam, Folddisco, Reseek"
},
{
"tag": "li",
"text": "Deep-twilight controls, 16 proteins (notebook 252): MMseqs2, jackhmmer, MMseqs2, three rounds, HH-suite (hhsearch), ProstT5 + Foldseek, hmmscan with Pfam, Folddisco, Reseek"
},
{
"tag": "li",
"text": "Short linear motifs (ELM) covered (notebook 253): hmmscan with Pfam, Folddisco, MMseqs2, search mode not recorded"
},
{
"tag": "li",
"text": "Domain finding, 15 relatives (this leaderboard): Folddisco, MMseqs2, search mode not recorded, Reseek"
},
{
"tag": "li",
"text": "Domain finding, 9 relatives: MMseqs2, search mode not recorded"
},
{
"tag": "li",
"text": "Domain finding, test set of 2 relatives: MMseqs2, search mode not recorded"
}
],
"data": {
"tables": [
{
"columns": [
"target species",
"identity",
"plddt",
"feature_type",
"feature_length_bin"
],
"rows": [
{
"tool": "folddisco",
"instances": {
"target species": 590559,
"identity": 516687,
"plddt": 121049,
"feature_type": 73872,
"feature_length_bin": 590559
}
},
{
"tool": "foldseek",
"instances": {
"target species": 1110504,
"identity": 939872,
"plddt": 231206,
"feature_type": 145722,
"feature_length_bin": 1085594
}
},
{
"tool": "hhblits",
"instances": {
"target species": 1158512,
"identity": 952047,
"plddt": 276686,
"feature_type": 181647,
"feature_length_bin": 1133694
}
},
{
"tool": "hmmer3_jackhmmer",
"instances": {
"target species": 1329803,
"identity": 952047,
"plddt": 276686,
"feature_type": 181647,
"feature_length_bin": 1133694
}
},
{
"tool": "hmmer3_phmmer",
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