MIToS_Scripts

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.

Scripts

• 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.

Installation

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:

julia 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:

julia using MIToS_Scripts joinpath(pkgdir(MIToS_Scripts), "scripts")

You can run them from that location or copy them to a directory in your PATH.

Usage

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:

bash 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:

bash julia Buslje09.jl -h

License

This project is licensed under the MIT License. See the LICENSE file for details.

References

1. 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.
2. 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.

Citing

See CITATION.bib for the relevant reference(s).