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URL: https://dx.doi.org/DOI:10.17504/protocols.io.bgdijs4e

Authors: Marcos Viana, Mauricio Mudadu, Adhemar Zerlotini

Summary: A1The Plantannot software provides several filters and a text search box that allows searching for molecules by its desired annotation features. These filters are needed to obtain PUFs and to try to relate them to abiotic stresses using RNA-seq expression data and co-expression networks. The Filters menu is separated in 8 fields, of those we are going to use only five: “Organism”, “Feature type”, “Orthology”, “Orthologs_coexpression” and “Analyses”. The “Feature Type” filter has three molecule types, from those the polypeptide box is the only that is going to be always checked and the others blank. By using the other 4 remaining filters, 6 protocols were created as examples of different ways to selecting PUFs. Protocol A: using lack of both homology and protein domain signatures. Protocol B: using lack of homology, presence of domain signatures - trying to select Domains of Unknown Function (DUF) from PFAM, and the text search “Unknown function”.Protocol C: using homology, lack of protein domain signatures and the text search “Unknown function”. Protocol D-F: same protocols of A-C but using ortholog groups to find homolog proteins with co-expression data related to abiotic stress.2Protocol C is intended do find PUFs from organisms that proteins are already public in the NCBI´s nr database and have no protein domains found by Interproscan. Proteins will be selected using the text search "Unknown function".

Affiliations: EMBRAPA, EMBRAPA, EMBRAPA

External URL: https://www.machado.cnptia.embrapa.br/plantannot

Version: 1

Publication Date: 2020

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