{
 "tool": "hhblits",
 "name": "HH-suite (hhsearch)",
 "kind": "builds a profile of a protein family",
 "compares": "Two profiles against each other. Here each profile was built from a single protein, not from a family alignment, because no UniRef30 database was given.",
 "needs": {
  "sequence only": true,
  "3D structure prediction": false,
  "GPU": false
 },
 "reference": "Single-protein profiles of the relative's proteome (Quest for Orthologs reference proteomes, release 2020_04), as an HH-suite database.",
 "score": "Bit score from hhsearch: higher ranks first.",
 "failure_modes": [
  "The run names this tool hhblits (its tool id), but it ran hhsearch on profiles of single proteins. HH-suite's usual use, with family alignments from UniRef30, was not run, so these numbers say nothing about it."
 ],
 "version": "HH-suite 3.3.0",
 "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/soedinglab/hh-suite",
 "container": "quay.io/biocontainers/hhsuite:3.3.0--h503566f_15 (sha256:4bf9bb5229de18f522a94f4443c19fdcbb0f0cb0e6ea92f5390aa170bcb0a24f)",
 "command": "ffindex_apply \\\n    human-38fdd87d_hhdb/db_a3m.ffdata human-38fdd87d_hhdb/db_a3m.ffindex \\\n    -d results.ffdata -i results.ffindex \\\n    -- hhsearch -i stdin -d zebrafish_hhdb/db -blasttab /dev/stdout -cpu 16 -v 0",
 "numbers_from": {
  "repo": "seanome/2024-kmerseek-analysis",
  "commit": "4a4b11714ddb740f8a7e324058b26bee8fb35af4",
  "filters": "pfam, raw, zebrafish"
 },
 "best_setting": "single_seq",
 "strong": [
  {
   "axis": "identity",
   "stratum": "no_homolog",
   "fmax": 0.03236195478661682,
   "n": 321,
   "other_tool": "foldseek",
   "other_setting": "3di_aa",
   "other_fmax": 0.027082308589475693,
   "margin": 0.005279646197141125
  },
  {
   "axis": "identity",
   "stratum": "40-60%",
   "fmax": 0.2482755120174425,
   "n": 563,
   "other_tool": "hmmer3_phmmer",
   "other_setting": "default",
   "other_fmax": 0.25193530617302773,
   "margin": -0.003659794155585233
  }
 ],
 "weak": [
  {
   "axis": "feature_length_bin",
   "stratum": "16-30",
   "fmax": 0.06589146154089374,
   "n": 271,
   "other_tool": "kmerseek",
   "other_setting": "wwmj5_k11_lcFalse",
   "other_fmax": 0.3297506857792661,
   "margin": -0.2638592242383723
  },
  {
   "axis": "feature_length_bin",
   "stratum": "31-60",
   "fmax": 0.08480095524712318,
   "n": 420,
   "other_tool": "kmerseek",
   "other_setting": "gbmr4_k21_lcFalse",
   "other_fmax": 0.23209537155652643,
   "margin": -0.14729441630940326
  }
 ],
 "cost_per_1000_queries": {
  "core_h_reserved_per_relative": 24.83871446596897,
  "n_relatives": 15,
  "database_build_core_h": 30.87333333333333,
  "database_build_gpu_h": null,
  "peak_rss_gb": 23.4,
  "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% 0.248 (n = 563), 60\u2013100% 0.283 (n = 1,289). If no, 20\u201330% 0.321 (n = 93), 30\u201340% 0.190 (n = 165). (Pfam truth set, raw calls, zebrafish (430 Mya) as the relative searched, setting single-protein profiles; 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 0.230 (n = 963), 121\u2013250 aa 0.298 (n = 504), 251 aa or more 0.417 (n = 277). If no, 16\u201330 aa 0.066 (n = 271), 31\u201360 aa 0.085 (n = 420). (Pfam truth set, raw calls, zebrafish (430 Mya) as the relative searched, setting single-protein profiles.)",
  "Can you spend about 24.8 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": "hhblits.md"
}