Protein Coverage API

This interface provides a means to calculate the sequence coverage of a named protein provided a given set of peptides are present.

Why have a protein coverage calculator?

Its nice to have.

USAGE

URL

./Coverage/?key=<str_access_key>&pro=<str_protein_name>&pep=<str_peptide_sequences>

Methods

GET or POST
Both methods are compatible with either http or https. It is recommended to use https as this encrypts your data and access token.

Request Parameters :: Summary
parameter type usage default accepted note
pro STRING required * *
pep STRING
hm BOOLEAN FALSE presence / absence
Request Parameters :: Detail
Responses:
code type content
200 success see example 1
400 bad request { error : "precursor mass (pm) parameter undefined" }
401 unauthorized { error : "key not found" }
429 too many requests { error : "too many requests" }

Note: unknown protein names will fail silently


EXAMPLES

Example 01

A simple example.

API Call
  http://pub.jvln.io/Coverage/?key=a1b-2c3-e4f-5&pro=ALBU_HUMAN&pep=ETCFAEEGKKLVAASQAALGL+CCKADDKETCFAEEGK+FQNALLVRYTKKVPQVSTPTLVEVSR+NYAEAKDVFLGMFLYEYAR
JSON Return Object
 {
  "protein": {
    "source": "uniprot_sprot",
    "protein_name": "ALBU_HUMAN",
    "protein_id": "P02768",
    "protein_desc": "Serum albumin",
    "organism": "Homo sapiens"
  },
  "result_time": "023ms",
  "result_data": {
    "coverage": 0.11986,
    "map": "mkwvtfisllflfssaysrgvfrrdahksevahrfkdlgeenfkalvliafaqylqqcpfedhvklvnevtefaktcvadesaencdkslhtlfgdklctvatlretygemadccakqepernecflqhkddnpnlprlvrpevdvmctafhdneetflkkylyeiarrhpyfyapellffakrykaafteccqaadkaacllpkldelrdegkassakqrlkcaslqkfgerafkawavarlsqrfpkaefaevsklvtdltkvhtecchgdllecaddradlakyicenqdsissklkeccekpllekshciaevendempadlpslaadfveskdvckNYAEAKDVFLGMFLYEYARrhpdysvvlllrlaktyettlekccaaadphecyakvfdefkplveepqnlikqncelfeqlgeykFQNALLVRYTKKVPQVSTPTLVEVSRnlgkvgskcckhpeakrmpcaedylsvvlnqlcvlhektpvsdrvtkccteslvnrrpcfsalevdetyvpkefnaetftfhadictlsekerqikkqtalvelvkhkpkatkeqlkavmddfaafvekCCKADDKETCFAEEGKKLVAASQAALGL"
  }
}
Example 02

Return the html formatted heat map. Note the red highlight near the end of the sequence indicating overlap from two distinct peptides.

API Call
  http://pub.jvln.io/Homology/?key=a1b-2c3-e4f-5&pro=ALBU_HUMAN&pep=ETCFAEEGKKLVAASQAALGL+CCKADDKETCFAEEGK+FQNALLVRYTKKVPQVSTPTLVEVSR+NYAEAKDVFLGMFLYEYAR&hm
JSON Return Object
{
  "protein": {
    "source": "uniprot_sprot",
    "protein_name": "ALBU_HUMAN",
    "protein_id": "P02768",
    "protein_desc": "Serum albumin",
    "organism": "Homo sapiens"
  },
  "result_time": "042ms",
  "result_data": {
    "coverage": 0.11986,
    "map": "<div style=\"font-family: Courier;\"><a style=\"color:#A0A0A0;\">M</a>
    <a style=\"color:#A0A0A0;\">K</a><a style=\"color:#A0A0A0;\">W</a>
    <a style=\"color:#A0A0A0;\">V</a><a style=\"color:#A0A0A0;\">T</a>
    <a style=\"color:#A0A0A0;\">F</a><a style=\"color:#A0A0A0;\">I</a>
    <a style=\"color:#A0A0A0;\">S</a><a style=\"color:#A0A0A0;\">L</a>
    <a style=\"color:#A0A0A0;\">L</a><a style=\"color:#A0A0A0;\">F</a>
    <a style=\"color:#A0A0A0;\">L</a><a style=\"color:#A0A0A0;\">F</a>
    <a style=\"color:#A0A0A0;\">S</a><a style=\"color:#A0A0A0;\">S</a>
    <a style=\"color:#A0A0A0;\">A</a><a style=\"color:#A0A0A0;\">Y</a>
    <a style=\"color:#A0A0A0;\">S</a><a style=\"color:#A0A0A0;\">R</a>
    <a style=\"color:#A0A0A0;\">G</a><a style=\"color:#A0A0A0;\">V</a>
    <a style=\"color:#A0A0A0;\">F</a><a style=\"color:#A0A0A0;\">R</a>
    <a style=\"color:#A0A0A0;\">R</a><a style=\"color:#A0A0A0;\">D</a>
    <a style=\"color:#A0A0A0;\">A</a>...</div>"
  }
}
Example HTML Heat Map