#pViz.js/VEP viewer: A browser side only application to view Ensemble Variant Effect Predictor output files The Ensembl Variant Effect Predictor produces '.vep' files with, among others, protein positioned features of variant.
We propose a tool to parse such an output, retrieve the protein sequence from Ensembl REST API, and align the features on the sequence, grouped by categories. ##Data sources Any '.vep' file can be fitted in the tool, either on of the test set or a loaded local files. Files with up to 1.5M lines can be parsed in a chrome browser in approximatively 10 seconds. ###Parsed features Any features with protein position are displayed. By default, only the protein with an 'ENSP.+' identifier can be displayed by default as the sequence is retrieved on a server (change the Ensembl REST url in the configuration menu to connect to a local store).
The field in the 'Extras' column are displayed when mousing over a feature.
The application can be used live at http://research-pub.gene.com/pviz/app/vep
##Usage Enter a gene name to display the related protein.
Zoom in the sequence by dragging the mouse and zoom out by double clicking.
Clone the project, then
npm install
bower install
#you may have to select a jQuery version: 2.1 looks perfect
#if grunt was not installed with -g
alias grunt=./node_modules/grunt-cli/bin/grunt
grunt server
Et Voilà
###Deploy
grunt build
rsync --recursive --delete dist/* your.host:/your/path/
##Authors This application is based on the versatile pViz.js: a dynamic JavaScript and SVG library for visualization of protein sequence features, written by Alexandre Masselot and Kiran Mukhyala, from the Bioinformatics & Computational Biology Department, at Genentech Inc. Research.
Thanks to Will McLaren for the contributions.
##Reference Please provide a reference to this application by citing: '''xxx.xx 2014'''
##Thanks to This app is aimed at demonstrating pViz.js library. But it would never have existed without a myriad of other useful an inspiring projects: d3.js, color brewer (and Mike Bostock implementation), grunt, bower, [bootstrap](http://getbootstrap.com/css, jQuery (and $.cookie), backbone.js, require.js, underscore.js, typeahead.js, Miso.dataset and a few others.
###License The library is distributed under a BSD license. Full description can be found in LICENSE.txt