TooT-SC.v1.svm.11

This tool predicts the substrate class of a given transporter. The class can belong to one of the following eleven categories [1] nonselective inorganic molecule [2] water [3] inorganic cation [4] inorganic anion [5] organic anion [6] organooxogyn [7] amino acid and derivatives [8] other Organonitrogen compound [9] nucleotide [10] organic heterocyclic [11] miscellaneous.

Details on ChEBI mapping is found on Substrate_ChEBI.csv file.

Input: transporter proteins sequences in Fasta format Output: the substrate class with highest probability, and the probabilities of the other classes.

Installation

git clone https://github.com/bioinformatics-group/TooT-SC.git
cd TooT-SC
wget https://tootsuite.encs.concordia.ca/databases/TooT-SC/v1.svm.11_db.tar.gz
wget https://tootsuite.encs.concordia.ca/datasets/TooT-SC/v1.svm.11_datasets.tar.gz
tar -xzf v1.svm.11_db.tar.gz
tar -xzf v1.svm.11_datasets.tar.gz
rm v1*

Use curl if you don't have wget.

FOLDERS

There are a number of folders that support the running of TranCEP and its outputs.

dataset/transporter_substrate_class

Contains both the training and the independent testing dataset if fasta format, the identifiers of independent testset is found under substrate_classes_indep.csv. The models were trained using the training dataset =(all dataset - independent testset)

intermediate_files

Contains the homology details needed to extract the features. Details of the Blast hits for each sequence is found here.

intermediate_files/Compostions: Contains the extracted MSA_TPAAC features of test set

db

Contains the database to be used when performing BLAST.

src

The scripts needed to use the tool.

HOW TO USE

• This tool requires that BLAST be pre-installed
• Usage: Rscript src/TooT_SC_V1_11.R -query=<input> [-TooTSC=<TooTSCdir>] [-out=<outdir>] [-db=<path to db>]
• <input> is your sequence input file in fasta format
• <out> is the output directory where you want the predicted results, formatted as csv
• <TooTSCdir> is the directory where the base TooT-SC files are located
• <db> is the directory where the database is stored
• MSA_PAAC features of each sequence in the test set is found under intermediate_files/Compositions/MSA_PAAC.csv