TooT-M

This tool predicts transporter proteins.

Input: proteins sequences in Fasta format Output: the predicted location,1=membrane, 0=non-membrane

The training dataset can be found here

FOLDERS

There are a number of folders that support the running of TooT-M and its outputs.

intermediate_files

Contains the homology details needed to extract the features. Details of the psiBlast 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_M.R -query=<input> [-TooTM=<TooTMdir>] [-out=<outdir>] [-db=<path to db>][-topcons2=<TOPCONS2 results path>]
• <input> is your sequence input file in fasta format
• <out> is the output directory where you want the predicted results, formatted as csv
• <TooTMdir> is the directory where the base TooT-M files are located
• <path to db> is the directory where the database is stored
• <TOPCONS2 results path> is the directory where TOPCONS2 results (.txt) is stored; results can be obtained by there available website [here](https://tootsuite.encs.concordia.ca/datasets/membrane/) or by downloading the tool as described [here](https://github.com/ElofssonLab/TOPCONS2)
• Pse-PSSM features (lambda in (0,1,...49) of each sequence in the test set is found under intermediate_files/Compositions/Testing/