In this tutorial, you will learn how to perform a structural genome annotation, and how to evaluate its quality. While for Maker you need to perform training steps for the ab-initio predictors, Funannotate is able to take care of that for you, which makes it much easier to use. Funannotate is also able to take into account repeated elements.įunannotate uses ab-initio predictors ( Augustus, SNAP, glimmerHMM, CodingQuarry and GeneMark-ES/ET (optional due to licensing)) to improve its predictions: these software tools are able to make gene structure predictions by analysing only the genome sequence with a statistical model. These sequences can come from public databases (like NR or GenBank) or from your own experimental data (transcriptome assembly from an RNASeq experiment for example). The evidences can be transcript or protein sequences from the same (or closely related) organism. 2021), it works by aligning as many evidences as possible along the genome sequence, and then reconciliating all these signals to determine probable gene structures. As other annotation tools like Maker ( Campbell et al. In this tutorial we will use a software tool called Funannotate ( Palmer and Stajich 2020) to annotate the genome sequence of a small eukaryote: Mucor mucedo (a fungal plant pathogen).Īs explained on Funannotate’s website, “it was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes”. Many genes also contain introns, and the limits of these introns (acceptor and donor sites) are not highly conserved. The sequences determining the beginning and the end of a gene are generally less conserved than the prokaryotic ones. This will allow you to skim your notations at a later date to locate key information and quotations, and to recall your thought processes more easily and quickly.Genome annotation of eukaryotes is a little more complicated than for prokaryotes: eukaryotic genomes are usually larger than prokaryotes, with more genes. Lastly, as you annotate, make sure you are including descriptions of the text as well as your own reactions to the text. Dedicate different tasks to each margin: Use one margin to make an outline of the text (thesis statement, description, definition #1, counter argument, etc.) and summarize main ideas, and use the other margin to note your thoughts, questions, and reactions to the text.Example: Yellow for definitions, orange for questions, and blue for disagreement/confusion. If you use highlighters, consider using different colors for different types of reactions to the text.Example: Underline for key points, highlight for vocabulary, and circle for transition points. Include a key or legend on your paper that indicates what each marking is for, and use a different marking for each type of information.As you annotate, use these strategies to make the most of your efforts: You can also annotate on post-its if you have a text you do not want to mark up. You can annotate by hand or by using document software. Annotating means you are doing the hard work while you read, allowing you to reference your previous work and have a clear jumping-off point for future work. Even if you regularly understand and remember what you read, annotating will help you summarize a text, highlight important pieces of information, and ultimately prepare yourself for discussion and writing prompts that your instructor may give you. However, annotating isn't just for people who feel challenged when reading academic texts. As you annotate, you should note the author's main points, shifts in the message or perspective of the text, key areas of focus, and your own thoughts as you read. This page will introduce you to several effective strategies for annotating a text that will help you get the most out of your reading.īy annotating a text, you will ensure that you understand what is happening in a text after you've read it. Sometimes called "close reading," annotating usually involves highlighting or underlining key pieces of text and making notes in the margins of the text. Annotating is any action that deliberately interacts with a text to enhance the reader's understanding of, recall of, and reaction to the text.
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