MIToS.jl

MIToS is an environment for Mutual Information (MI) analysis and implements several useful tools for Multiple Sequence Alignments (MSAs) and PDB structures management in the Julia language.

This is the documentation for MIToS v2 in Julia v1. If you are using MIToS 1.0 in Julia 0.4, please read this documentation instead.

Modules

MIToS tools are separated on different modules, related to different tasks.

MSA : This module defines multiple functions and types for dealing with MSAs and their annotations. It also includes facilities for sequence clustering.

PDB : This module defines types and methods to work with protein structures from PDB.

SIFTS : This module allows access to SIFTS residue-level mapping of UniProt, Pfam and other databases with PDB entries.

Information : This module defines residue contingency tables and methods on them to estimate information measure from MSAs. It includes functions to estimate corrected mutual information (ZMIp, ZBLMIp) between MSA columns.

Pfam : This module use 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 an Utils module with common utils functions and types used in this package.

Citation

If you use MIToS, 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

Leloir Institute Foundation

Structural Bioinformatics Unit, Leloir Institute Foundation. Av. Patricias Argentinas 435, CP C1405BWE, Buenos Aires, Argentina