The Template predictor Predictor API runs blastBLAST, sparksxSparksX, and hhsearchHHsearch. 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
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Quickstart
Command Line Examples
Submit a template predictor job:
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cyrus engine submit template-predictor SECVENGGFCPDPEKMGDWCCGRCIRNECRNG |
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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
– hhsearchHHsearch alignment file
sequence.hhr
–.hhr alignment file
target.pssm
– pssmBLAST 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