Alamut® Visual: Focus on each track

This page is the written transcript of the video tutorial entitled "Alamut® Visual: Focus on each track", available here

In this video, we will focus on the different functionalities of Alamut Visual through the different tracks.

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If you wish to display several genes simultaneously, you can launch several Alamut Visual instances from the same computer. In order to do so, you need to go to the menu Application/ New Alamut Visual instance: a new window will be opened.

Let’s open for instance the gene TP53. In Alamut Visual, you have the possibility to move the tracks upwards or downwards like this, or to hide them like this.

You can also display the tracks you want through the Menu/Tools/ Options/Display and customize your main screen by checking or unchecking the different boxes.

Let’s go back to the different tracks:

Here is the Nucleotide Conservation track, it gives you some information about the conservation’s score for each nucleotide, with the PhastCons and PhyloP scores.

Below is the transcript track where you can create your owns mutations.

Here are the dbSNP and SwissProt Variants tracks. The synonymous variants are indicated in green, the non-synonymous variants are indicated in yellow.

If you click with the left button, you will see the consequence of the mutation on the protein sequence. If you click with the right button, you will get a report concerning the selected variant.

Variants identified by SwissProt are displayed here. If you click with the right button, you will be directed to the SwissProt variant internet page.

This track shows the ExAC variants: a blue rectangle indicate a deletion or a delins. A blue nucleotide indicates a substitution, If multiple single nucleotide variants are reported at the same position, a blue background is displayed along with a “+” sign, like this one. When you pass the mouse over a nucleotide, populations’ allele frequencies and estimated read depth are displayed. If you right click on a substitution, you will open the ExAC internet page concerning the selected variant.

Below, you have the ClinVar track, it shows variants of clinical interest. In red are the certainly pathogenic variants. In orange are the likely pathogenic variants, in green are the certainly benign variants and in yellow are the variants of an uncertain clinical significance. When you right click on a variant, you will obtain a detailed report. You can filter your variants based on review status or by phenotype.

If you have a HGMD professional license, you will be able to access HGMD through Alamut Visual. If you right click on an HGMD variant, you’ll be able to see PubMed Citations, to go to the HGMD variant page, to see the HGMD gene page, or make an internal mutation in Alamut Visual.

Alamut Visual offers you the possibility to visualize data coming from Cosmic, even if you don’t have a Cosmic license. A blue nucleotide indicates a substitution, a triangle indicates an insertion or duplication, and a line indicates a deletion. You can select the type of tissues you want to display here. You can also define a permanent set of preferred tissues here. When you right click on a nucleotide, you will obtain a detailed report like this one.

Here you have the Protein Domains track. We can see that this domain covers this region.

Below we have the Orthologues Alignments tracks which show the amino acids conservation through different species.

You are able to load BAM files from your computer or a web server. In order to do so, you just need to click on “application”, “load BAM alignment” from files for instance and select the appropriate file. The alignment will be then displayed in a new track on your screen. You can see the targeted region here that corresponds by default to the exons of the transcript. This is the coverage and the depth of coverage. The maximum depth of coverage for the gene is reported here. You have the reads alignments displayed below. You can customize the BAM visualization by clicking on this button. For instance, you can squish the reads or condense them.

When loading BAM files, corresponding VCF files will be automatically loaded if they have the same name. If you right click, you’ll get the VCF properties. You can go from a variant to another one like this. You also have the possibility to see the BAM alignment statistics here.

Finally, this track allows you to indicate your Private Annotations, for instance, the location of your Primers. To create your private annotation, you need first to create the dataset. In order to do this you need to select the nucleotides involved. Then, click right and select add dataset. The dataset will appear here. Then you just need to right click and select “Annotation”. If you want to indicate the sequence direction you can choose to put an arrow. You can change the color and add some comments and then you can save it. You’ve just created your Private Annotation. If you click on it, you’ll display it. You can of course delete it.

In order to use Alamut Visual to its full potential, we strongly recommend you to read the user manual. To do this, go to the menu “help”, “software documentation”; there you will have access to the Alamut Visual manual.

If you have any questions regarding the use of Alamut Visual, you can contact our support team by email via the menu “Help”/”Contact Support”.

Don’t hesitate to visit our website to request a free 30-day trial of Alamut Visual.

For an introduction on how to use Alamut Visual, please watch our video Alamut Visual: how to use the software.