Template predictor 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.
Inputs
sequence – the sequence to run template predictor on
Command Line Examples
Submit a template predictor job:
cyrus 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")
Outputs
sparksx-cambyses-aln.json – sparksX alignment file
hhsearch-cambyses-aln.json – hhsearch alignment file
sequence.hhr – hhr file
target.pssm – pssm file
results.tsv – results from hhsearch and sparksX parsed into TSV format
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
zs12