{
 "tool": "foldseek",
 "name": "Foldseek",
 "kind": "compares 3-D shape letters (3Di)",
 "compares": "Predicted 3-D shapes. Each residue of an AlphaFold model gets one of 20 shape letters (3Di) from its local fold. The shape letters are aligned together with the amino acids.",
 "needs": {
  "sequence only": false,
  "3D structure prediction": true,
  "GPU": false
 },
 "reference": "AlphaFold models of the relative's proteome (Quest for Orthologs reference proteomes, release 2020_04 accessions), as a Foldseek database.",
 "score": "Bit score: higher ranks first. The E-value cutoff was 10.",
 "failure_modes": [
  "A protein with no AlphaFold model cannot be searched. Five relatives have no Foldseek rows at all (chimpanzee, cow, dog, opossum, western clawed frog): not run.",
  "AlphaFold models of long proteins come in overlapping pieces (F1, F2, ...). The task script moves piece n's coordinates 200 x (n - 1) residues along the protein; if a piece started elsewhere, its calls would land in the wrong place. Checked against the real piece starts: not measured."
 ],
 "version": "Foldseek 10.941cd33",
 "licence": "GPL-3.0",
 "commercial_use": "Yes. If you distribute a changed version, you must release its source under GPL-3.0 too.",
 "licence_url": "https://github.com/steineggerlab/foldseek",
 "container": "quay.io/biocontainers/foldseek:10.941cd33--h5021889_1 (sha256:1156a052f31b2afb85257c02e83a962f559c9752273fe1064ab735f90ac29d1a)",
 "command": "foldseek search \\\n    human-38fdd87d_fsdb/db zebrafish_fsdb/db result foldseek_tmp \\\n    --threads 16 \\\n    -e 10.0 \\\n    --max-seqs 1000",
 "numbers_from": {
  "repo": "seanome/2024-kmerseek-analysis",
  "commit": "4a4b11714ddb740f8a7e324058b26bee8fb35af4",
  "filters": "pfam, raw, zebrafish"
 },
 "best_setting": "3di_aa",
 "strong": [
  {
   "axis": "identity",
   "stratum": "no_homolog",
   "fmax": 0.027082308589475693,
   "n": 321,
   "other_tool": "hhblits",
   "other_setting": "single_seq",
   "other_fmax": 0.03236195478661682,
   "margin": -0.005279646197141125
  },
  {
   "axis": "identity",
   "stratum": "30-40%",
   "fmax": 0.16701190421314652,
   "n": 165,
   "other_tool": "mmseqs2_iterative",
   "other_setting": "s7",
   "other_fmax": 0.20886402027992682,
   "margin": -0.0418521160667803
  }
 ],
 "weak": [
  {
   "axis": "feature_length_bin",
   "stratum": "16-30",
   "fmax": 0.004474321206119519,
   "n": 271,
   "other_tool": "kmerseek",
   "other_setting": "wwmj5_k11_lcFalse",
   "other_fmax": 0.3297506857792661,
   "margin": -0.32527636457314657
  },
  {
   "axis": "feature_length_bin",
   "stratum": "31-60",
   "fmax": 0.034179736822508223,
   "n": 420,
   "other_tool": "kmerseek",
   "other_setting": "gbmr4_k21_lcFalse",
   "other_fmax": 0.23209537155652643,
   "margin": -0.19791563473401821
  }
 ],
 "cost_per_1000_queries": {
  "core_h_reserved_per_relative": 0.1287018481407259,
  "n_relatives": 10,
  "database_build_core_h": 0.26666666666666666,
  "database_build_gpu_h": null,
  "peak_rss_gb": 1.5,
  "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% 0.164 (n = 563), 60\u2013100% 0.241 (n = 1,289). If no, 20\u201330% 0.268 (n = 93), 30\u201340% 0.167 (n = 165). (Pfam truth set, raw calls, zebrafish (430 Mya) as the relative searched, setting shape letters + amino acids; subsets with at least 30 true instances.)",
  "Do you have a 3D structure prediction for every protein you want to annotate? If not, Foldseek cannot search the proteins without one.",
  "Can you spend about 0.129 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": "foldseek.md"
}