TOA aims to establish workflows geared towards plant species that automate the extraction of information from genomic databases and the annotation of sequences. TOA uses the following databases: Dicots PLAZA 4.0, Monocots PLAZA 4.0, Gymno PLAZA 1.0, NCBI RefSeq Plant and NCBI Nucleotide Database (NT) and NCBI Non-Redundant Protein Sequence Database (NR). Although TOA was primarily designed to work with woody plant species, it can also be used in the analysis of experiments on any type of plant organism. Additionally, NCBI Gene, InterPro and Gene Ontology databases are also used to complete the information.
TOA has a user-friendly front-end where researchers can perform the following tasks simply with a few clicks: i) download biochemical and biological data from genomic databases; ii) design the annotation pipeline that implements the most appropriate workflow for the experiment they are analyzing; iii) view statistics and graphics of results; and iv) track the status of processes during execution.
Refer to the TOA manual (https://github.com/GGFHF/TOA/blob/master/Package/TOA-manual.pdf) for installation instructions, a description of the software and examples of use. Also, you can see the paper:
Mora‐Márquez, F., Chano, V., Vázquez‐Poletti, J. L., & López de Heredia, U. (2021). TOA: A software package for automated functional annotation in non‐model plant species. Molecular Ecology Resources, 21(2), 621–636. DOI: 10.1111/1755-0998.13285
This software has been developed by:
GI Sistemas Naturales e Historia Forestal
(formerly known as GI Genética, Fisiología e Historia Forestal)
Dpto. Sistemas y Recursos Naturales
ETSI Montes, Forestal y del Medio Natural
Universidad Politécnica de Madrid
https://github.com/ggfhf/The software package TOA is available for free download from the GitHub software repository (https://github.com/GGFHF/TOA) under GNU General Public License v3.0.