Scuchloroplast Localization Prediction using AdaBoost Predictor
#Cite:
SCLAP: An Adaptive Boosting Method for Predicting Subchloroplast Localization of Plant Proteins Vijayakumar Saravanan and P.T.V. Lakshmi. OMICS: A Journal of Integrative Biology. February 2013, 17(2): 106-115. doi:10.1089/omi.2012.0070.
#Installation
Linux OS (a) Download DualPred from github. (b) Extract the files to the desired location. (c) Provide executable permission to SCLAP and Batch_SCLAP file (if it doesn't have executable rights). (d) make sure java 1.6 or higher is installed in your system. (e) make sure PERL 5.0 or higher version is installed in your system. (f) Make sure standalone BLAST (version 2.2.30+) is installed and executables added to the path.
#Instructions Execute the program by typing the following command after installation
(a) For Single protein run ./SCLAP [input sequence file] [output file name] ex: ./SCLAP Seq_raw_in Out1
Note: The input sequence file should contain single sequence in RAW format. FASTA format is not accepted!. For Batch sequence prediction use Batch_SCLAP.
(b) For Batch Protein run ./Batch_SCALP [input_mult_protein_file] ex: ./Batch_SCLAP Mult_input
Note: The input sequence file may contain multiple protein sequences in FASTA format. For batch submission RAW format is not accepted. The output for the batch submission will be stored as file named with first 11 characters of the corresponding FASTA header.
#Important Note:
This tool is to predict the subchloroplast location of a chloroplast protein. It doesnt validate whether the input protein is a Chloroplast protein or not. Hence, it is highly advised to input a chloroplast protein. Providing a unkown protein to this tool still predicts a subchloroplat location, but it doesnt make any sense. For details refer the article.