CKSAAP-Palm: A tool for predicting palmitoylation sites from protein sequences

References#

• 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.

Manual#

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.

Data File#

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.

Input File#

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.

Command Line#

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".

For examle:

CKSAAP-Palm  Pos.txt  Neg.txt   MUNN.fasta  100  0.0000015  Low

Software and Data#

• CKSAAP-Palm.zip

Contacts#

Any question or advice please email to wangxiao_bo_happy@126.com

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