{
 "tool": "kmerseek",
 "name": "kmerseek",
 "kind": "counts shared k-mers in a reduced alphabet",
 "compares": "Short words of k letters (k-mers) shared between two proteins. First, each amino acid is replaced by a letter from a smaller alphabet, for example H for hydrophobic and P for polar. Two proteins can then match where their residues differ but their pattern of residue types is the same.",
 "needs": {
  "sequence only": true,
  "3D structure prediction": false,
  "GPU": false
 },
 "reference": "An index of the relative's proteome (Quest for Orthologs reference proteomes, release 2020_04), built once per alphabet and k-mer length.",
 "score": "region_enrichment: the number of k-mers the region shares with the target divided by the number expected by chance (fold enrichment). Higher ranks first. A region was kept when either test passed: its own score was at least 1.3, or the whole query protein's p-value was at most 0.05.",
 "failure_modes": [
  "A feature shorter than k residues contains no complete k-mer, so it cannot be found. Figure 2 above shows how Fmax changes with region length.",
  "The task script records a kmerseek search that exits with an error as a search with no hits, so a crash would look like a miss. How often that happened in this run: not measured.",
  "Setting hp_thomas_dill2 k33 was scored, but no trace row holds its search task, so its cost is not measured, and the scoring task for it was not found either."
 ],
 "version": "kmerseek 0.3.1 (printed in the search log)",
 "licence": "MIT",
 "commercial_use": "Yes.",
 "licence_url": "https://github.com/seanome/kmerseek",
 "container": "docker.io/olgabot/kmerseek:2026-08-24-reduced-alphabets",
 "command": "kmerseek search \\\n    --alphabet hp_thomas_dill2 \\\n    --ksize    24 \\\n    --query    UP000005640_9606.fasta \\\n    --target   zebrafish.hp_thomas_dill2.k24.lcfalse.kmerseek.rocksdb \\\n    --threshold         0.0 \\\n    --min-shared-kmers  2 \\\n    --max-query-pvalue  0.05 \\\n    --min-region-score  1.3",
 "numbers_from": {
  "repo": "seanome/2024-kmerseek-analysis",
  "commit": "4a4b11714ddb740f8a7e324058b26bee8fb35af4",
  "filters": "pfam, raw, zebrafish"
 },
 "best_setting": "gbmr4_k21_lcFalse",
 "strong": [
  {
   "axis": "feature_length_bin",
   "stratum": "16-30",
   "fmax": 0.280694003473648,
   "n": 271,
   "other_tool": "hhblits",
   "other_setting": "single_seq",
   "other_fmax": 0.06589146154089374,
   "margin": 0.21480254193275422
  },
  {
   "axis": "feature_length_bin",
   "stratum": "31-60",
   "fmax": 0.23209537155652643,
   "n": 420,
   "other_tool": "hmmer3_phmmer",
   "other_setting": "default",
   "other_fmax": 0.09545667362809032,
   "margin": 0.1366386979284361
  }
 ],
 "weak": [
  {
   "axis": "feature_length_bin",
   "stratum": "251+",
   "fmax": 0.05,
   "n": 277,
   "other_tool": "hmmer3_phmmer",
   "other_setting": "default",
   "other_fmax": 0.4770249187378286,
   "margin": -0.4270249187378286
  },
  {
   "axis": "identity",
   "stratum": "20-30%",
   "fmax": 0.0,
   "n": 93,
   "other_tool": "hmmer3_phmmer",
   "other_setting": "default",
   "other_fmax": 0.35875364786222397,
   "margin": -0.35875364786222397
  }
 ],
 "cost_per_1000_queries": {
  "core_h_reserved_per_relative": 0.0551695984561716,
  "n_relatives": 15,
  "database_build_core_h": 0.14666666666666667,
  "database_build_gpu_h": null,
  "peak_rss_gb": 5.2,
  "hardware": "Stanford Sherlock, SLURM partition hns"
 },
 "questions": [
  "Is the closest same-family domain in the relative you will search at least 40% identical, for most of your proteins? If yes, Fmax here is 40\u201360% 0.005 (n = 563), 60\u2013100% 0.297 (n = 1,289). If no, 20\u201330% 0.000 (n = 93), 30\u201340% 0.000 (n = 165). (Pfam truth set, raw calls, zebrafish (430 Mya) as the relative searched, setting gbmr4, k = 21; subsets with at least 30 true instances.)",
  "Are the features you care about longer than 60 residues? If yes, Fmax here is 61\u2013120 aa 0.208 (n = 963), 121\u2013250 aa 0.098 (n = 504), 251 aa or more 0.050 (n = 277). If no, 16\u201330 aa 0.281 (n = 271), 31\u201360 aa 0.232 (n = 420). (Pfam truth set, raw calls, zebrafish (430 Mya) as the relative searched, setting gbmr4, k = 21.)",
  "Can you spend about 0.0552 core-hours per 1,000 proteins for each relative you search? That is the measured mean per relative; see \"Cost per 1,000 queries\" below."
 ],
 "markdown": "kmerseek.md"
}