{
 "tool": "hmmer3_phmmer",
 "name": "phmmer",
 "kind": "aligns amino-acid letters",
 "compares": "Amino-acid letters, one query protein against each protein of the relative, scored with a substitution matrix the way BLAST does but with HMMER's model of insertions and deletions.",
 "needs": {
  "sequence only": true,
  "3D structure prediction": false,
  "GPU": false
 },
 "reference": "The relative's proteome (Quest for Orthologs reference proteomes, release 2020_04), as a FASTA file.",
 "score": "Domain bit score: higher ranks first. The E-value cutoff was 10.",
 "failure_modes": [
  "Failure modes specific to phmmer: not measured in this run."
 ],
 "version": "HMMER 3.4",
 "licence": "BSD 3-clause (HMMER)",
 "commercial_use": "Yes.",
 "licence_url": "https://github.com/EddyRivasLab/hmmer/blob/master/LICENSE",
 "container": "quay.io/biocontainers/hmmer:3.4--hb6cb901_4 (sha256:7a2b317b8d2fd3650b4924a8482cddeb940d4a0746c6a1501ff03ac1b7439e0c)",
 "command": "phmmer \\\n    --domtblout /dev/stdout \\\n    --tblout /dev/null \\\n    -o /dev/stderr \\\n    --noali \\\n    -E 10.0 \\\n    --cpu 8 \\\n    UP000005640_9606.fasta UP000000437_7955.fasta",
 "numbers_from": {
  "repo": "seanome/2024-kmerseek-analysis",
  "commit": "4a4b11714ddb740f8a7e324058b26bee8fb35af4",
  "filters": "pfam, raw, zebrafish"
 },
 "best_setting": "default",
 "strong": [
  {
   "axis": "identity",
   "stratum": "20-30%",
   "fmax": 0.35875364786222397,
   "n": 93,
   "other_tool": "mmseqs2_iterative",
   "other_setting": "s7",
   "other_fmax": 0.3369499538756736,
   "margin": 0.021803693986550354
  },
  {
   "axis": "plddt",
   "stratum": "50-70",
   "fmax": 0.3246883921695622,
   "n": 748,
   "other_tool": "mmseqs2_seqseq",
   "other_setting": "s7",
   "other_fmax": 0.31014870966192065,
   "margin": 0.014539682507641538
  }
 ],
 "weak": [
  {
   "axis": "feature_length_bin",
   "stratum": "16-30",
   "fmax": 0.042035123644865974,
   "n": 271,
   "other_tool": "kmerseek",
   "other_setting": "wwmj5_k11_lcFalse",
   "other_fmax": 0.3297506857792661,
   "margin": -0.2877155621344001
  },
  {
   "axis": "feature_length_bin",
   "stratum": "31-60",
   "fmax": 0.09545667362809032,
   "n": 420,
   "other_tool": "kmerseek",
   "other_setting": "gbmr4_k21_lcFalse",
   "other_fmax": 0.23209537155652643,
   "margin": -0.1366386979284361
  }
 ],
 "cost_per_1000_queries": {
  "core_h_reserved_per_relative": 0.41653677725822014,
  "n_relatives": 15,
  "database_build_core_h": null,
  "database_build_gpu_h": null,
  "peak_rss_gb": 4.9,
  "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% 0.252 (n = 563), 60\u2013100% 0.308 (n = 1,289). If no, 20\u201330% 0.359 (n = 93), 30\u201340% 0.199 (n = 165). (Pfam truth set, raw calls, zebrafish (430 Mya) as the relative searched, setting default options; 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 0.250 (n = 963), 121\u2013250 aa 0.329 (n = 504), 251 aa or more 0.477 (n = 277). If no, 16\u201330 aa 0.042 (n = 271), 31\u201360 aa 0.095 (n = 420). (Pfam truth set, raw calls, zebrafish (430 Mya) as the relative searched, setting default options.)",
  "Can you spend about 0.417 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": "hmmer3_phmmer.md"
}