API Accessing Terminus programmatically

Terminus comes with a web API, allowing to execute the prediction remotely in any program. Any programming and scripting language wich allows HTTP connections can be used.

Instructions

To use the api you will need to make an http POST request to an address wich encodes your choice of predictor and the data format. The sequences data must be submitted in the request body.

There two ways of using this API:

FASTA/CSV

You can send the sequences data in FASTA format and you will receive the result in CSV. The resulting CSV is the same that the one outputed in the website, when you press the Download as CSV yellow button.

JSON

You can send the sequences data in JSON format and you will receive the result in JSON. The exact format is described below.

Use the configuration tool below to generate the URL automatically. Several examples are provided below.

Configuration tool

1. Choose the method

2. Choose the predictor

3. Grab the url

Json Format

Input

The input must be a list of objects, where each object corresponds to a protein. Object keys/values are:

• id: protein ID
• seq: protein sequence

For instance, a result for two proteins could be:

[ 
  { "id":"prot1", "seq":"MAKLKLAKALAKA" },
  { "id":"prot2", "seq":"MDEDEDEEDEDE" }
]

Output

The output format is also a list of object, where each object corresponds to a protein. Object keys/values are:

• id: protein ID (as sent by the user)
• seq: protein sequence (as sent in the input data)
• prediction: string prediction as reported in the web interface.
• n-terminus: the predicted n-terminus
• cleaved: prediction of initial methionine excision
• cleaved: prediction of acetylation

For instance, a result for a single protein could be:

[
  {
    "id":"prot1",
    "seq":"MAKLKLAKALAKA",
    "prediction":"cleaved-not-acetylated",
    "acetylated":"false",
    "cleaved":"true",
    "n-terminus":"AKLK"
  }
]

Examples of programs

Coming soon...

Bash script

Coming soon...