Jaevalen

The Proteomics API

Developed by SoCal Bioinformatics Inc.


Overview

Let's face it, proteomics is fragmented when it comes to bioinformatics tools. To make matters worse, most tools are initially developed only to be left unsupported and often most have convoluted or missing documentation. Jaevalen is an API resource that alleviates the 3 most annoying aspects of proteomic bioinformatics:

By colocating all of the above in one place, Jaevalen will keep things organized, simple and hopefully productive.

Motivation

The Jaevalen API and Data Viewer were built to provide a concise and accessible method for doing everyday bioinformatics calculations in proteomics, regardless of coding platform or expertise. Use this graphical interface to explore your data, or programmatically access the APIs in your everyday code. Documentation along with examples are provided at the above mentioned site, along with a few code snippets to show how you can incorporate the API into your code.

My goal with Jaevalen is to create a scalable, performant, bioinformatics resource with a minimal API that does the really really annoying stuff, and leaves the rest up to you.

This API is currently deployed as a test BETA v0.8.7.38 . Meaning that we are continuing to test and develop all of the underlying methods and algorithms. Each is currently working as expected in all test scenarios, however, corner cases do exists and we strive to find and eliminate them was they popup.

To access this collection of APIs you will need an Access Token which can be obtained for free at jaevalen.com.


SEARCH


TANDEM SEARCH

The API for JAEVALEN Search allows for the interrogation of single spectra to identify the sequence from a large data base consisting of all known consensus sequences and known variants together with a multitude of post translational modifications.


HOMOLOGY SEARCH

This homology engine is geared towards proteomics, as opposed to genomics (i.e. blastp) that use genetic-based substitution matrices and scoring statistics that typically hide highly redundant sequences. In addition this engine is significantly faster than any current methods. The API for JVLN Homology allows for the Single Amino Acid Polymorphism (SAP) retrieval of any given amino-acid combination, with special consideration for proteotypic sequences.


ISOSPECTRAL SEARCH

This homology engine is designed to facilitate the identification of de novo sequencing methods.



COMPUTE


PROTEOLYSIS

This interface provides a means to generate the insilico predicted peptides expected for a given proteotypic digest.


PROTEIN COVERAGE

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


PEPTIDE FRAGMENTATION

This interface provides a means to calculate the insilico predicted fragmentation patterns expected for proteotypic peptides with flexable vairaible modifications.


MRM TRANSITION ANALYSIS

The MRM transition analysis runs an insilico analysis of all possible conflicts providing a report of the count of total conflicts found using the same engine used in the Tandem Search API.




Examples using the Tandem Search API

Refer to the specific API's about page for usage definitions and expected outputs.

R Code
install.packages('httr')
library(httr)

url  <- 'https://pub.jvln.io/Tandem/'

params <- list(
    key='a1b-2c3-e4f-5',
    pm=569.78,
    pz=2,
    pks=paste(
        c(175.1,262.1,304.16,361.18,375.17,503.22,508.25,631.32),
        collapse = '+'
    ))

response <- POST(url, body = params,)

code <- status_code(response)

data <- content(response)
Python Code
pip install requests
import requests 
  
url = 'https://pub.jvln.io/Tandem/'
  
params = {
    'key'='a1b-2c3-e4f-5',
    'pm'=569.78,
    'pz'=2,
    'pks'='+'.join(
        [175.1,262.1,304.16,361.18,375.17,503.22,508.25,631.32]
        )
    } 
  
response = requests.post(url = url, params = params) 

code = response.status_code

data = response.json()