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