Alamut® Visual: How to use the software

This page is the written transcript of the video tutorial entitled "Alamut® Visual: How to use the software", available here

Interactive Biosoftware offers the most comprehensive solution for variant clarification, interpretation and reporting, on a single interface.

Alamut Visual is a mutation interpretation software designed to help scientists interpret human genome variants. Today, Alamut Visual includes more than 27,000 protein-coding genes, non-protein coding genes and pseudogenes which are frequently updated. Gene information is gathered from different public databases like NCBI, UCSC and EBI.

When you launch Alamut Visual, you need to select the gene you want to work on. If the gene wanted is not available in the Alamut Visual database, you can email us a “gene request” with this button. You can customize the shortcuts list with the genes you usually work with. Let’s take TP53 for example.

There are several assemblies available: you need to select the transcript you want to work on. You have its overview just here. The introns are yellow and the exons are blue. You can also check the preferred transcript box so that it will be automatically selected the next time you load the gene. And then you click on “ok”. The data are loaded from our server.

You need to focus on the part you want to study. In order do this, you have several possibilities. You can select the part you want to have a look at, like this and then zoom-in. You can navigate around the locus or you can directly click on the exon number you want to work on.

Here you have an overview of the transcript. Here you have the genome sequence, the nucleotide conservation track, and here we have the mRNA track where we can create some mutations.

In order to create a mutation, you can directly click on this button at the top of the screen, or just select a nucleotide, click with the right button and select “mutation”. You need then to choose the type of mutation you want to create, substitution, deletion, insertion, duplication or delins. Let’s make a substitution with a nucleotide change from G to A.

The variant window appears. You have some information about the mutation you’ve just created.

First you have the HGVS nomenclature, the location of the variant, the type – here we have a substitution- the coding effect; we have created a missense mutation.

With this button you can compare amino acids between the wild sequence and the mutated sequence.

If the variation you’ve created is known and reported in general populations, you will have some information indicated here. You’ll also have some information from mutation databases such as HGMD, if you have a professional license or ClinVar. You have PubMed citations concerning this gene and the mutations in this gene.

Here you have the Missense Predictions algorithms. Here are reported the automatically computed results for Align GVGD, SIFT and Mutation Taster. You can click this button to open all the windows at the same time, and directly access the missense predictions websites. You can also access each missense predictions tools’ website separately by clicking on the tool button directly. The form is automatically pre-filled by Alamut Visual, you just have to submit the results!

Here you can classify your variant based on its pathogenicity. You have the ability to choose the class for the report; either the 5 classes report, which goes from “certainly not pathogenic” to “certainly pathogenic”, or the 3 classes report which goes from “not pathogenic” to “pathogenic”.

Please note that the pathogenicity class is not automatically computed because Alamut Visual doesn’t have any information about the patient, his phenotype, disease, or his environment.

You can write some comments here. You can also create some occurrences for each patient, to indicate the patient ID, the family ID, and any relevant information regarding this patient.

Let’s choose “Not pathogenic” by clicking on this button, you will access a detailed mutation report including all the relevant information that will help you decide about the variant pathogenicity. You can save it, print it or copy it.

We will now create a new mutation in order to visualize the predictions in the splicing window. Let’s create for instance an intronic mutation in +4 and let’s choose a substitution with a nucleotide change from A to T.

You can then have a look at the splicing window by clicking on this button. Here is the reference sequence and here is the mutated sequence.

Several splicing predictors are available in Alamut Visual. Vertical blue bars represent splicing donor signal predictions; vertical green bars represent the acceptor signal predictions. Known constitutive splicing patterns are displayed as blue triangles for donor sites or green triangles for acceptor sites.

You can also highlight differences between the reference sequence and the mutated sequence here.

We can see that the predictions at the splicing junction are reduced; this suggests that these variants alter splicing. Finally, you have here the splicing predictions options settings and you can also generate a report clicking this button.

Let’s go back to the main screen: you have different tracks coming from different reliable sources such as dbSNP and Swissprot, Exac, ClinVar, HGMD and COSMIC. In the “options” window, you can display the tracks you want. Just go to the Menu/Tools/ Options/ Display.

You also have the possibility to load BAM files along with VCF files. To get further details about these tracks, please have a look at our next video “Alamut Visual: focus on each track”.

This is the Protein Domains track, the Orthologues Alignment track and finally the Private Annotations track where you can enter your own annotations.

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 launch several Alamut Visual instances if you want to display several genes 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.

On the home page, you’ll find some information about your license, about the software updates and any relevant information concerning Alamut Visual. Please visit this page regularly to be informed about the latest news regarding Alamut Visual.

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 further details about the different tracks, please watch our video Alamut Visual: focus on each track.