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PSO-AA

Protein Sequence Optimizer – Aminoacid sequence

PSO-AA (Aminoacid sequence) is an API endpoint to optimize the sequence of a protein for expression in a host organism. While other available tools use a deterministic approach and return always, and only, one solution, PSO uses a stochastic approach. This means that PSO can perform a wider exploration of the solution panorama, instead of being restricted to the same solution over and over again.
From a single input sequence PSO generates a population of solutions that are recombined, scored and selected over and over again to obtain a final pool of optimized solutions. The key for the optimization is the selection of best performing sequences, that we choose based on the target organism, on the analysis of structures and adapt to custom needs like forbidden restriction sites.
Once added the input parameters and run the API, the request will be added to our tasks queue, and the system will return a task id to use in the successive phases of the process. By means of the task id previously generated, you can access the status of the computation while running and the outcomes once completed.

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POST Parameters:

input_sequence : The sequence to be optimized, either a DNA or an amino acid sequence.

input_organism : The host organism. Currently supported organisms: E. coli, Mammalian cell, S. rimosus, S. coelicolor, S. cerevisiae.

restriction_sites_to_avoid : A list of restriction enzymes to avoid. Please list the name of the enzymes to forbid. This parameter supports the commercially available enzymes from the REBASE database (listed in the commdata file).

GET Parameters

task_id : The task id to access the request status and results

Example

POST Input payload

{
    "input_sequence": "APMAEGGGQNHHEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYI",
    "target_organism": "E. coli",
    "population_n": 100,
    "generation_n": 10,
    "mfe_weight": 1.5,
    "mfe_weight_downstream": 1.5,
    "cai_weight": 0.5,
    "cai_weight_downstream": 1.5,
    "gc_weight": 0,
    "target_gc": 50,
    "restriction_sites_to_avoid": [
        "Kpn2I",
        "EcoRI"
    ],
    "custom_forbidden_strings": [
        "ATTATTAT"
    ]
}

POST response

{
  "id": "1e8e7cd9-a50f-4ef7-8330-c6b12f967b85"
}

GET endpoint

 https://api-testing.officinae.bio/api/v1/tasks/{task_id}
 e.g. https://api-testing.officinae.bio/api/v1/tasks/1e8e7cd9-a50f-4ef7-8330-c6b12f967b85

GET Response

{
  "input_sequence": "APMAEGGGQNHHEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYI",
  "target_organism": "E. coli",
  "output_sequence": "GCTCCAATGGCTGAAGGCGGTGGTCAAAACCATCACGAAGTTGTGAAATTCATGGATGTGTACCAGCGTTCCTACTGCCACCCGATCGAAACCCTGGTTGACATCTTCCAGGAATACCCAGACGAAATCGAATATATC",
  "output_score": 0.9434255947536685,
  "output_gc": 48.55,
  "restriction_sites_to_avoid": [
    "Kpn2I",
    "EcoRI"
  ],
  "remaining_sites": 0,
  "custom_forbidden_strings": [
    "ATTATTAT"
  ]
}