Using MenDeVar via RESTful API

The MenDeVAR (Meningococcal Deduced Vaccine Antigen Reactivity) Index tool can be accessed via the PubMLST RESTful API, allowing it to be incorporated in to an analysis pipeline.

Documentation for the API call can be found at http://bigsdb.readthedocs.io/en/latest/rest.html#db-schemes-scheme-id-sequence.

The following examples assume that you have a FASTA file containing a bacterial genome assembly called contigs.fasta in your current directory.

Command line (curl) | Perl | Python

curl

The curl command can be used to make API calls using the Linux command line. The FASTA file needs to be base64 encoded and embedded within a JSON payload. This can be done with the following commands.

Output is in JSON format, and looks like the following:

Perl

Output

Bexsero:
Result: exact match
Notes: fHbp_peptide: 1 is exact match to vaccine variant - peptide sequence match (PMID:27521232)

Trumenba:
Result: cross-reactive
Notes: fHbp_peptide: 1 is cross-reactive to vaccine variant - data derived from MEASURE assays (PMID:29535195), and SBA assays (PMID:22569484, PMID:22718089, PMID:22871351, PMID:23114369, PMID:23352429, PMID:26407272, PMID:26707218, PMID:26803328, PMID:26835974, PMID:26974889, PMID:27745812, PMID:27846061, PMID:28196734, PMID:28566335, PMID:29236639)

Python

Output

Bexsero:
Result: exact match
Notes: fHbp_peptide: 1 is exact match to vaccine variant - peptide sequence match (PMID:27521232)

Trumenba:
Result: cross-reactive
Notes: fHbp_peptide: 1 is cross-reactive to vaccine variant - data derived from MEASURE assays (PMID:29535195), and SBA assays (PMID:22569484, PMID:22718089, PMID:22871351, PMID:23114369, PMID:23352429, PMID:26407272, PMID:26707218, PMID:26803328, PMID:26835974, PMID:26974889, PMID:27745812, PMID:27846061, PMID:28196734, PMID:28566335, PMID:29236639)