Overview

Gene prediction or gene finding is an essential step aimed at identifying gene regions in genomes, whether these genes are non-coding or protein-coding.There are many assembled genomes in databases used in various genetic studies, but few of these genomes have annotations.In addition, only a very small set of genomes are updated annotations.Therefore, in research dealing with genomes from databases, the step of re-annotation is essential.Therefore, we present this course with practical, step-by-step, screen-recorded content for the use of gene prediction software with more than one example.This course provides a set of protocols that have been modified and implemented without any errors.The course includes all organisms from prokaryotes to eukaryotes.The course Includes protein-coding genes and non-coding genes.In addition to evaluating the resulting prediction from gene prediction software.There are generic programs that are used with prokaryotes and eukaryotes:tRNAscan-SE is used to predict tRNA genes. It is characterized by the fact that it does not require a computer with high capabilities.Infernal is used with rfam database to predict all non-coding genes but is more accurate in predicting rRNA and other non-coding RNA genes. It is characterized by the fact that it does not require a computer with high capabilities, but it takes a long time.There are programs for eukaryotic organisms:BRAKER, which is used to predict protein-coding genes using the ab initio method, also uses extrinsic evidence from mapped RNA-seq and protein to support and increase accuracy. Requires a computer with high capabilities.GeMoMa is used to predict protein-coding genes by homology and also uses extrinsic evidence from mapped RNA-seq. Requires a computer with high capabilities.There is a program for prokaryotic organisms:Prokka is used to predict protein-coding and non-coding genes using the ab initio method and also uses extrinsic evidence from the protein. It does not require a high-powered computer.Finally, the BUSCO program is used to evaluate the prediction of protein-coding genes in prokaryotic and eukaryotic organisms. It does not require a high-powered computer.All programs have been screen-recorded on the ubuntu distribution since it is the most famous Linux distribution.It is best to install the Ubuntu distribution on your device or create virtual ubuntu using a virtual box in order to implement the course practically on your device.You will eventually get the protocols in text format that you can apply with genomes from the database in a graduation project, in a research paper, or in a poster.

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