Quick Start Tutorial for MonViso Reloaded

This tutorial will walk you through the process of preparing input files and running MonViso Reloaded for mutation analysis.

Step 1: Download the UniProt databases

Download and decompress the following files:

• Database of isoforms
• Database of split variances

Remember the directory containing the .fasta files. It will be one of the parameters required to run the software.

Step 2: Prepare Input Files

You will need to create two files: mutations.txt for listing the mutations and parameters.dat for specifying various parameters and paths used by MonViso Reloaded.

Writing mutations.txt

Create a text file named mutations.txt and fill it with your mutations of interest, formatted as shown below:

GRIN1
R 844 C
Ala 349 Thr
Pro 578 Arg
Ser 688 Tyr
Tyr 647 Ser

GRIN2B
E413G
C436R
M1342R
L1424F
PRO1439ALA

Each section starts with the gene name, followed by lines specifying the original amino acid, its position, and the mutated amino acid.

Writing parameters.dat

Create a text file named parameters.dat and specify the configuration for your analysis as follows:

DB_LOCATION= [path to database location]
COBALT_HOME=[path to cobalt binaries]
HMMER_HOME=[path to HMMER binaries]
MODELLER_EXEC=[command to run modeller e.g., mod10.5]
PESTO_HOME=[path to cloned PeSTo repo]
RESOLUTION=4.50
SEQID=25
HMM_TO_IMPORT=100
MODEL_CUTOFF=5
PDB_TO_USE=10
NUM_OF_MOD_WT=1
NUM_OF_MOD_MUT=1
W_STRUCT=10
W_MUT=10

Step 3: Run the command

monviso_reloaded -i mutations.txt -o out -p parameters.dat