Demo: Exploring the Aedes aegypti (Yellow fever mosquito) genome in Ensembl

This step-by-step guide explores the new Ensembl site (beta.ensembl.org) using the Aedes aegypti (Yellow fever mosquito) genome as an example.

Ensembl Browser
43 steps
6 minutes

Ensembl

Navigate to [https://beta.ensembl.org/](https://beta.ensembl.org/)

You have different buttons (Apps) available on the launch bar at the top. The first app "Species Selector" can be used to add as many species as you want. Your species will then be available across all apps.

The next button is for "Genome Browser". You can use this app to look at genes & transcripts in their genetic context and download this data. It can be opened from the launch bar at the top of every page.

Then we have "Entity viewer". Use this app to get gene & transcript information. Entity viewer pages will give information on your gene of interest and as always you can download this data in different formats.

The "BLAST" app can be used to compare DNA or protein sequences across species.\ You can add up to 30 sequences and up to 25 species at a time to view significant sequence matches across species.

The "Ensembl VEP" app can be used to annotate genetic variants and find out their consequences.\ You can paste your variants into the text box or upload variant files of up to 250 MB in size.

Click on the "Question mark" to see Ensembl Beta help and documentation pages.

We will click on the "Species selector" app to find and select *Aedes aegypti* (Yellow fever mosquito) and find more information about the genome assembly.

We have some popular vertebrate and non-vertebrate species shown on this page.

Type "mosquito" in the "Find a species" text box and click on "Find".

25 mosquito genomes are available, which are listed below.

We will select *Aedes aegypti* (Yellow fever mosquito). Tick the box to the left of the common name.

Click "Add" to add the Yellow fever mosquito genome to your species list.

Click "Yellow fever mosquito" in your species list for more information about this genome assembly.

This opens a panel that lists information about the genome assembly, including the number of genes and variants in the genome...

...a link to the assembly submission...

...and the annotation provider.

You can retrieve whole-genome files by clicking on the "Get files" icon.

Click on "Close" to return to the "Species selector" app.

Let's search for the AAEL010883 gene in *Aedes aegypti* (Yellow fever mosquito). Click on "Find a gene".

Enter "AAEL010883" into the text box and click "Go".

Click the gene ID "AAEL010883".

You can view the gene in the "Genome Browser" or "Entity Viewer" app. Let's start with the Genome Browser.

The Genome Browser view shows the Yellow fever mosquito AAEL010883 gene in the genomic location context. The genomic features (e.g. AAEL010883) within this location are represented on horizontal tracks across the genome. Click the "AAEL010883" track to view more information about the gene.

The Ensembl canonical transcript "AAEL010883-RB" is shown at the top of the view by default. The Ensembl Canonical transcript is a single, representative transcript identified at every locus.

Click "Download" to export the data from this view.

From these options, you can export genomic and protein sequences for the gene and associated transcripts.

Click ">" in the "Action bar" on the right-hand side to open the "Track panel".

Here, you can turn tracks on/off and explore other options. Click "+2" to list the other AAEL010883 transcripts.

Click the "..." icon next to the Ensembl canonical transcript to open the transcript panel.

This panel gives you more detailed information about the transcript, including the sequence. Select "Sequence" to view the transcript sequence and "Download" to export the sequence.

Click "x" in the upper right-hand corner to close the transcript panel.

Let's now explore the "Entity Viewer" app, which allows you to view detailed information about annotation features. In the Genome Browser, click the "AAEL010883" track and select "Entity Viewer".

The "Entity Viewer" app icon at the top is highlighted to indicate which app you are currently in.

The "Transcripts" tab provides detailed information on the individual AAEL010883 transcripts, associated exons and translations. You can click on the individual transcripts to collapse and expand the information panel.

Click the "Gene function" tab to explore interactions, functional annotations and external references for the gene.

You can click on the protein domains to see more information about the protein families, including hyperlinks to the associated entries.

You can collapse and expand the individual transcript panels by clicking on the amino acid length.

Switch to the "Gene relationships" tab to view comparative genomics analyses related to AAEL010883. The Ensembl Compara pipeline has found 31 homologues.

Let's find the homologue that is most similar to our gene of interest in terms of protein similarity. Click "% Protein similarity" to sort the Homology table by the header.

You can explore additional information about the entity of interest (in this case the AAEL010883 gene) by expanding the right-hand panel.

Here, you can find a description of the gene, any synonyms (if available), the biotype and links to external references.

You can have your say in the development of the new Ensembl site! On the homepage, you can leave your feedback by clicking the bottom left icon!