CKSAAP-Palm: A tool for predicting palmitoylation sites from protein sequences
- Last updated: May 28, 2010
- Xiao-Bo Wang, Ling-Yun Wu, Yong-Cui Wang, and Nai-Yang Deng. Prediction of palmitoylation sites using the composition of K-spaced amino acid pairs. Protein Engineering, Design, and Selection, in press, 2009.
CKSAAP-Palm is a tool for predicting palmitoylation sites based on protein sequence. The program is implemented in C. The win32 console version is provided.
The "Pos.txt" and "Neg.txt" are the positive and negative training sequence fragments respectively. The user can replace these files by theri own training data.
The input file is in the FASTA format. Each file can includes one or multiple sequences. Each sequence must have the amino acid "C". More sequences require more computer resource. For typical computer, the number of sequences less than 50 should be fine.
The output will be saved into "Result.txt" in the same directory.
CKSAAP-Palm <Positive Data> <Negative Data> <Input File> <C> <Gamma> <Cutoff>where <Positive Data> <Negative Data> <Input File> are specified above, and <C> <Gamma> <Cutoff> is the paramters.
The paramter C can be any positive number. The Gamma should be between 0.015 and 0.0000015. The Cutoff should be "Low" or "High".
CKSAAP-Palm Pos.txt Neg.txt MUNN.fasta 100 0.0000015 Low
Software and Data#
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