Plot Protein Application

Link to Application:

Plot Protein

Description:

This tool takes mutation information at the protein level and plots out the mutation above the schematic of the protein. It also plots the domains as well as providing a table (under table tab) with the annotation of domains and post-translational modification for each amino acid change.

Notes:

All files should be referring to the same isoform of the protein. This is imperative for drawing the plot correctly. Also, images can be saved by right clicking on the plot and saving as a picture.

For best results, run this application in FireFox or Google Chrome.

Required files:

Mutation file: tab-delimited file containing 5 columns (ProteinId, GeneName, ProteinPositionOfMutation, ReferenceAminoAcid, AlternateAminoAcid) NO HEADER NEEDED FOR THIS FILE

Protein architecture file: tab-delimited file containing 3 columns (architecture_name, start_site, end_site). This file NEEDS the header and it is the same as what was previously written. This information can be downloaded from the HPRD (http://hprd.org/) or can be whatever you have gleaned from the literature.

Post-translational modification file: This is a tab-delimited file with only one column and that is the site. This file NEEDS a header and is as previously written.

Additional Information Required:

Length of Protein: The length in amino acids of your protein

Additional Options:

Name of Query: Any name you want to show up on the plot

X-axis Tick Size: How far apart you want the x-axis ticks

Zoom In: You can choose whether or not you want to zoom in to a particular part of the protein

Example Input Files:

Please see attached at the bottom of the page example files for this application. The length of the protein in for the test files is 463

Example Output Without Zoom:

Example Output With Zoom