Template Predictor

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.

Quickstart

Command Line Examples

Submit a template predictor job:

cyrus engine submit template-predictor SECVENGGFCPDPEKMGDWCCGRCIRNECRNG

Python Examples

Submit a template predictor job:

from engine.template-predictor.client import TemplatePredictorClient client = TemplatePredictorClient() job_id = client.submit(sequence="SECVENGGFCPDPEKMGDWCCGRCIRNECRNG")

Inputs

  • --sequence (str)

    • 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