Client Server

GTXplorer: A portal to navigate and visualize the evolutionary information encoded in fold A glycosyltransferases

This repo includes the GTXplorer web database files and can be downloaded to deploy a local copy of GTXplorer.

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Configurations

To change labels, and visibility of the controls, you may edit the web-react/src/gta.settings.json file.

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Running the Project Locally

1. Download this repository to your desired directory

   ​ by clicking on the green code button at the top to download as zip or use the following command:

   ​ git clone https://github.com/esbgkannan/GTxplorer.git

2. Start the Alignment View server

   1. cd web-react
   2. npm install (if necessary, run rm -rf node_modules before this command)
   3. npm start (it starts the server on http://localhost:3000, you can change the port in the web-react/src/package.json file).

3. Start the GTXplorer project with both tree and alignment view

   1. cd web

      (Optional): If the local server is running on an address except http://localhost:3000,

      1. Edit the src property value in the following line in index.html:

         <iframe id="react_frame" src="http://localhost:3000/" width="550" height="550" frameborder="0" scrolling="yes" style="width: 100%">

      2. Edit the SERVER_ADDRESS variable value in web/src/JS/index.js

   2. Start the project on a local server:

      serve -s .

      Note: If serve is not installed. Install it by running npm install -g serve.

      Now, you can navigate to http://localhost:5000/ to view the website.

4. (Optional) Download large data files

   ​ Get the data files that are available for download through the web version of GTXplorer using the following script. Run the script from the GTXplorer folder.

   ​ cd GTxplorer

   ​ bash download.sh

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Tutorial

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Description of the data files:

All the complete datasets for GTXplorer are in the db_files folder.

This folder is organized into the following:

1. Fasta/

   Includes individual files per GTA clade, family and subfamily with all the GTA domain sequences for that level.

2. FastaFull/

   Includes individual files per GTA clade, family and subfamily with all the GTA full length sequences for that level.

3. Tables/

   Contains tab delimited files with extensive information for all GTA sequences in a given level (clade,family or subfamily).

Other directories with relevant data for gtXplorer:

1. Domains/

   For each of the 53 GTA families, this directory contains tables with the domain organization information (one shortened easily readable version and an extended version with more detailed information).

2. Tax/

   This directory includes files with taxonomic distribution information for all GTA clades, families and subfamilies.

3. WeblogoDomain/

   Includes png images of the weblogs for the alignments of sequences from GTA clades, families and subfamilies.

Other files:

1. Hierarchy.tsv

   Tab delimited file defining the entire hierarchy of the GTA fold.

2. GTA_Tree.csv

   A csv file for the generation of KinView style viewer.

3. GTA_Clade.json

   Includes details to display in the cards for the 9 major clades.

4. GTA_Fam.json

   Includes details to display for the 53 major GTA families (in the labels of the GTA tree)

5. GTA_SubFam.json

   Incudes details for the GTA subfamilies.

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For questions, comments and requests, please contact the ESBG lab at UGA.

Natarajan Kannan: nkannan@uga.edu

Rahil Taujale: rtaujale@uga.edu

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Updates

• v1.0.0
  • First packaged beta version.

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Citation

If you find this tool helpful, please cite:

Rahil Taujale, Saber Soleymani, Amitabh Priyadarshi, Aarya Venkat, Wayland Yeung, Krys Kochut and Natarajan Kannan. GTXplorer: A portal to navigate and visualize the evolutionary information encoded in fold A glycosyltransferases. Preprint.

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License

This work is licensed under the MIT license.