This repository is a Command line interface bash script for Linux and Mac. This program will fetch high confident PTM sites at peptide and protein level based on user-defined ptmRS probability cut-off. A summary of the number of PTM sites that qualify the said cut-off will be generated. Also, a PTM window consisting of 7 amino acids upstream and downstream of the PTM site will be provided. This window can be used for motif enrichment or to identify conserved motifs. The PTM-window can also be used for the comparision with PhosphoSitePlus database (Nov 12, 2018).
HOW TO USE:
Clone or Download the repository.
Usage:
user@userGitHub$ bash PTM_Pro.sh <probability_cut-off> <database> <organism> <input.txt>
Example: bash PTM_Pro.sh 75 HsRefSeq75_NXP_cont.nr.062516.fasta human Ex_human_PTM_PSMs.txt
Options:
<probability_cut-off>: probability cut-off ( 0 to 100)
<database>: Formatted database (Click here for available databases or refer the header format)
<organism>: For comparission with PhosphoSitePlus
<input.txt>: Your input text file.
For detailed instructions for formatting and processing your input, please follow the published web portal PTM-Pro.
Please Cite: Patil, A. H., Datta, K. K., et al., Dissecting Candida pathobiology: Post-translational modifications on the Candida tropicalis proteome. 2018. OMICS: A Journal of Integrative Biology. [PubMed]