A Julia Package to Analyze Protein Sequences, Structures, and Evolutionary Information
Modules
MIToS tools are separated into different modules for different tasks.
- MSA: This module defines multiple functions and types for dealing with Multiple Sequence Alignments (MSAs) and their annotations. It also includes facilities for sequence clustering and shuffling, among others.
- PDB: This module defines types and methods to work with protein structures from different sources, such as the Protein Data Bank (PDB) or AlphaFold DB. It includes functions to superpose structures, measure the distance between residues, and much more.
- Information: This module defines residue contingency tables and methods on them to estimate information measures. This allow to measure evolutionary information on MSAs positions. It includes functions to estimate corrected mutual information (ZMIp, ZBLMIp) between MSA columns, as well as conservation estimations using Shannon entropy and the Kullback-Leibler divergence.
- SIFTS: This module allows access to SIFTS residue-level mapping of UniProt, Pfam, and other databases with PDB entries.
- Pfam: This module uses the previous modules to work with Pfam MSAs. It also has useful parameter optimization functions to be used with Pfam alignments.
- Utils: MIToS has also a Utils module with common utils functions and types used in different modules of this package.
Citation
If you use MIToS [1], please cite:
Diego J. Zea, Diego Anfossi, Morten Nielsen, Cristina Marino-Buslje; MIToS.jl: mutual information tools for protein sequence analysis in the Julia language, Bioinformatics, Volume 33, Issue 4, 15 February 2017, Pages 564–565, https://doi.org/10.1093/bioinformatics/btw646
Older MIToS versions
You can change the MIToS version of the documentation at the bottom left of this site—the older version available is MIToS 2.0. If you are using MIToS v1 in a version of Julia pre-1.0, please read this older documentation instead.
Acknowledgments
MIToS was initially developed at the Structural Bioinformatics Unit of the Fundación Instituto Leloir (FIL) in Argentina. Its development now continues at the Molecular Assemblies and Genome Integrity group of the Institute for Integrative Biology of the Cell (I2BC) in France.
We want to thank all contributors who have helped improve MIToS. We also thank the Julia community and all the MIToS users for their feedback and support.
