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  • License MIT

An bioinformatics tool to predict and analyze DNA, RNA or protein sequences.

Package Exports

  • bioinformatics-hub

This package does not declare an exports field, so the exports above have been automatically detected and optimized by JSPM instead. If any package subpath is missing, it is recommended to post an issue to the original package (bioinformatics-hub) to support the "exports" field. If that is not possible, create a JSPM override to customize the exports field for this package.

Readme

Bioinformatics-Hub

This is an open source project used for protein and nucleotide analysis and prediction. At the current stage, this package can perform analysis and prediction based on mutiple protein or nucleotide sequences in FASTA format. We will add pdb analysis in the future.

In version 1.x.x, this application can:

  • Read multiple protein or nucleotide sequences.
  • Remove any numbers, blanks, and comment line (line start with ";") in each sequence.
  • Retrieve a specific sequence by squenceId.
  • Retrieve all sequence Ids.
  • Retrieve all sequences as javascript object indexed by sequence Ids.
  • Scan and predict protein/nucleotide motifs in multiple sequences provided by user in FASTA format.

How to use this package

Installation

Running this package requires nodeJS environment. Run the below commend to install this package into your project.

npm install --save bioinformatics-hub

Basic usage example

To be updated ...

Handle mulitple FASTA sequences

To be updated ...

Prediction protein/nucleotide motifs

To be updated

https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=BlastHelp

Handle invalid input

  • invalid data type
  • invalid fasta sequences
  • invalid charactor
  • numbers inside of a string

Version changes

  • 1.0.x
    • in progress.
  • 1.0.0
    • Read multiple protein or nucleotide sequences.
    • Remove any numbers, blanks, and comment line (line start with ";") in each sequence.
    • Retrieve a specific sequence by squenceId.
    • Retrieve all sequence Ids.
    • Retrieve all sequences as javascript object indexed by sequence Ids.
    • Scan and predict protein/nucleotide motifs in multiple sequences provided by user in FASTA format.

For internal Bioinformatics-Hub developers

High Level Design

high level design

Test

Jest is used to perfom all unit tests in this repository. Tests are written in the test folder using the idential file structure in the .js files in the src folder. Use this command to run all the unit tests:

npm run test

Note: Each commit in master branch must sure to have 0 test failure.

ESLint

We use ESLint to enforce js format. ESLint rules is defined in .eslintrc.json file. Run this command to check js format issues: 

npm run lint

Run this command to check js format and auto-fix issues:

npm run lint-fix