Template Predictor API

The Template Predictor API runs BLAST, SparksX, and HHsearch. It will output a HHR sequence alignment file, one alignment file from hhsearch and one from sparksx, and a PSSM. It will also output a TSV which is a parsed version of these files.

Command Line Interface

Examples

Submit a template predictor job:

lev engine submit template-predictor SECVENGGFCPDPEKMGDWCCGRCIRNECRNG

Flags

  • --sequence (str) (Required)
    • Sequence to run template predictor on

Python Interface

Examples

Submit a template predictor job:

from engine import EngineClient

client = EngineClient()
client.authorize()

job_id = client.submit_template_predictor(
    sequence="SECVENGGFCPDPEKMGDWCCGRCIRNECRNG"
)

Flags

  • sequence (str) (Required)
    • Sequence to run template predictor on

Outputs

  • sparksx-cambyses-aln.json
    • sparksX alignment file
  • hhsearch-cambyses-aln.json
    • HHsearch alignment file
  • sequence.hhr
    • .hhr alignment file
  • target.pssm
    • BLAST PSSM file
  • results.tsv
    • TSV format of results parsed from hhsearch and sparksX

Notes

Output File interpretation

  • results.tsv
    • homology_probability
      • <60%: low confidence in homology modeling
      • 60-80%: major modeling required
      • >80%: high confidence in homology modeling
    • template_coverage
      • <50%: homology modeling will lead to divergent models
      • 50-70%: homology modeling will lead to fairly converged models
      • >70%: homology modeling will lead to very converged models
    • sequence_identity
    • gaps_over_12_residues
      • The number of gaps greater than 12 residues long in each template
    • positions_in_no_templates
      • A list of all positions which are missing from each template

Updated: