Step 1: Create an annotation database To create a database, first create a new folder.This tutorial provides instruction on three methods for transferring annotations between sequences.
A Plasmid Editor Tutorial Zip File Into GeneiousDOWNLOAD THE TRANSFERRING ANNOTATIONS TUTORIAL Tutorial Instructions Geneious Prime tutorials are installed by either Dragging and dropping the zip file into Geneious Prime or using File Import From File.Transferring Annotations Between Sequences Note: To complete the tutorial with the referenced data please download and install the tutorial above into Geneious Prime. Revised December 2019: This tutorial describes new features available in Geneious Prime 2020 and later. Annotations provide descriptive information about the structure andor function of features within DNA, RNA or protein sequences. Annotations may sometimes be grouped into tracks and can span multiple intervals, for example, when a CDS comprises multiple exons. In Geneious Prime, annotations are displayed graphically in the Sequence Viewer panel where they can be edited. Their display can be controlled via the Annotations Tracks tab. Annotations are depicted graphically as boxes or as arrows if the feature has a defined orientation. See our Knowledge Base post for more information on standard annotationsfeatures used in Geneious and GenBank. Geneious Prime has numerous tools and external plugins for adding new annotations to sequences, most of which can be found under the Annotate and Predict menu. This tutorial focuses only on methods for transferring existing annotations between sequences. There are three ways to transfer annotations between sequences within Geneious Prime, which can be summarized as being either: by homology Using Annotate from Database Using a custom database useful for annotating unaligned sequences with a diverse selection of annotations by homology Using Transfer Annotations Useful for transferring annotations to a reference or consensus sequence in an alignment or assembly, where homology is shared across some or all regions of the alignment by alignment Using Copy To Useful for transferring individual annotations or for shorter alignments where homology is shared across the entire length of the alignment This tutorial provides exercises demonstrating how to use each of the above methods. If you are unsure about which method to use then we recommend you use the Annotate from Database tool. To install, go to Menu Tools Plugins and choose MAFFT Multiple Alignment from the list of Available Plugins. Exercise 1: Live annotation using Annotate from Database Exercise 2: Live annotation using Transfer Annotations Exercise 3: Transferring annotations using Copy to Summary Exercise 1: Transferring annotations Using the Annotate from Database tool The Annotate from Database tool, as the name suggests, requires that you create a database of annotations that are likely to be found in your sequence. A database comprises a folder containing annotated sequences of interest. The database may contain a sequence with multiple annotations, for instance a related genome, andor annotated sequences that encode single features. In Geneious Prime 2019.2 onwards, unannotated sequences can also be used in the Source folder, and Geneious will treat these as though they have a single miscfeature annotation across their entire length. Improvements in Geneious Prime 2020 and later In Geneious Prime 2020 and later the Annotate from database tool includes a new Adjust CDS boundaries option which allows transferred CDS annotation boundaries to be automatically adjusted to match, within specified limits, the start and stop codons on a corresponding predicted ORF. This is on by default and will be used in the exercise below. Users of older versions of Geneious will need to check and if required, manually adjust CDS ends (see Exercise 2). Annotation of a sequence using an annotation database In this exercise we will take an unannotated Kiwi mitochondrial genome and annotate it using a simple database comprising an annotated Emu mitochondrial genome sequence.
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