IAP Binding Motif (IBM) scoring algorithm for identifying IBMs present in protein and peptide sequences.
IBMScore using a position weighted scoring matrix derived from data in Kurakin et. al. J. Mol Recognit (2007), Eckelman et. al. Cell. Death Differ. (2008), and Chen et. al. biorxiv (2023). A full description of the methods used to develop this scoring algorithm can be found in XXXXXX.
Programming Language: Python This code was specifically written in Python 3.7.5
Required Python Packages: None
IBMScore can be run in the command-line, where inputs are specified using an arguement parser. An example run is:
run IBMScore.py -in IgA.fasta
Each of the parser flags are described below and can also be displayed using -h:
-in --Input_FASTA_File Required Name of the text file containing the FASTA sequence of the protein of interest. Carot should not be in same line as sequence, UniProt format preferred.
-out --Output_File Optional Name of the text file that will contain the results. Use when you want the output saved to a file instead of printing to the terminal.
-cut --Cutoff_Value Optional Cutoff value above which a peptide is considered to be an IBM. The default is 0.5.
-pwm --PWSM Optional Supply a specific position weighted score matrix for score calculation.
-all --Return_All Optional Use of this flag will return all scored peptides instead of just peptides above the cutoff.