Important! Please write the name of your kinase in ALL CAPS so the R script can recognize it! Thank you! If your kinase is one of the following kinases, please use this form of its name: ABL, ARG, BTK, CSK, FYN, HCK, JAK2, LCK, LYN, PYK2, SRC, SYK, YES, FLT3 So for example if your kinase is ARG please use ARG and not ABL2
This tool is intended for use in conjunction with KinaMine.jar and Negative Motif Finder. Using the outputs from those two functions (The Positive and Negative substrates as well as the Substrate Background Frequency) this tool calculates optimal substrates
Positive Substrates The Positive Substrates file should be formatted such that accession numbers are in the third column, the indibidual amino acids of the phosphorylated motif takes up columns 4 to 18, with the phosphorylated Tyrosine in column 11 and the phosphorylated Tyrosine marked as xY instead of simply Y. The list of motifs and accession numbers should start on the second row and not the first.
Negative Substrates This file should be formatted such that accession numbers are in the first column, the entire motifs are in the second column, and the list of accession numbers plus motifs should start on the second row
Substrate Background Frequency list Accession numbers and percentages starting on row 2. Accession numbers in column 1, A-Y amino acids in columns 2-21, number of Y in column 34, number of pY in column 35.