MIToS_Scripts.jl is a command-line interface (CLI) script collection designed to facilitate various bioinformatics tasks. Any researcher with basic terminal knowledge can easily utilize these scripts without Julia's coding experience.
- Buslje09.jl: Calculates the corrected Mutual Information (MI/MIp) as described by Buslje et al., 2009.
- BLMI.jl: Computes corrected mutual information using BLOSUM62-based pseudocounts, as described in the MIToS publication (Zea et al., 2016).
- Conservation.jl: Calculates Shannon entropy and Kullback-Leibler divergence for each column in a Multiple Sequence Alignment (MSA).
- DownloadPDB.jl: Downloads gzipped files from the Protein Data Bank (PDB).
- Distances.jl: Computes inter-residue distances in a PDB file.
- SplitStockholm.jl: Splits a Stockholm file containing multiple alignments into separate compressed files for each MSA.
- AlignedColumns.jl: Creates a Stockholm file with aligned columns from a Pfam Stockholm file, removing insertions, and saves the mapping of residue numbers in UniProt and the original MSA columns.
- PercentIdentity.jl: Calculates the percentage identity between all sequences in an MSA and provides statistics such as mean, median, and minimum values.
- MSADescription.jl: Provides statistics for a given Stockholm file, including the number of columns, sequences, and clusters after Hobohm I clustering at 62% identity. It also reports the mean and standard deviation of sequence coverage and gap percentage.
To install MIToS_Scripts.jl, you only need Julia 1.9 or later installed on your
system. Executing julia
in the terminal to open the Julia REPL, and finally, run the
following command:
using Pkg
Pkg.add("https://github.com/MIToSOrg/MIToS_Scripts.jl")
Then, you can get the location of the installed scripts by running the following command:
using MIToS_Scripts
joinpath(pkgdir(MIToS_Scripts), "scripts")
You can run them from that location or copy them to a directory in your PATH
.
You can execute each provided script from your command line. For example, to run the Buslje09.jl
script—if you are located in the folder where it is the scripts—use:
julia Buslje09.jl input_msa_file
Refer to the documentation of each script for specific usage instructions; you can access
it by running the script with the --help
or -h
flag:
julia Buslje09.jl -h
This project is licensed under the MIT License. See the LICENSE file for details.
- Buslje, C. M., Santos, J., Delfino, J. M., & Nielsen, M. (2009). Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information. Bioinformatics, 25(9), 1125-1131.
- Zea, D. J., Anfossi, D., Nielsen, M., & Marino-Buslje, C. (2017). MIToS. jl: mutual information tools for protein sequence analysis in the Julia language. Bioinformatics, 33(4), 564-565.
See CITATION.bib
for the relevant reference(s).