Alamut Visual Plus™

Deep Dive into Genomic Variants
Overview Key Features Resources Support Contact
Overview
Key Features
Resources
Support
Contact

Explore variants on a genomic scale

Alamut Visual Plus™ enables deep assessment of variants on a genomic scale, empowering clinical researchers to make accurate decisions for their data interpretation.

Alamut Visual Plus™ is a full genome browser designed to help researchers investigate variations of the human genome. ​

The software combines a wide set of external data with high-quality missense and splicing predictors in one unique interface. As a result, Alamut Visual Plus™ decreases the time and effort required to assess the pathogenicity of genomic variants while maximizing lab workflow efficiency.

Furthermore, visualization of different bioinformatics formats is now available in parallel, including Sanger, VCF, BED, and BAM files. Researchers can now also benefit from a simultaneous display of multiple genes in separate tabs.​ ​

Data pooling and knowledge sharing
Fig 1. Advanced features accelerate complex variant assessment
A universal health data analytics platform for a decentralized approach to healthcare
Fig 2. Comprehensive full-genome browser integrating different features, genomic and literature databases

Cutting edge technology

Alamut Visual Plus™ is used in renowned university medical centers, hospitals and private genetic analysis laboratories worldwide. Highly appreciated by its users, the software accelerates complex and time-consuming assessment of variants thanks to its user-friendly interface and integrated features.​

It includes regularly curated information from different genomic (e.g. ClinVar, dbSNP, COSMIC) and scientific data sources (e.g. Mastermind® and PubMed®), up-to-date ACMG/AMP guidelines, and HGVS nomenclature.

World renowned curated genomic and literature databases, up-to-date guidelines, high-quality missense and splicing predictors are only some of the multiple integrated features of Alamut Visual Plus™ that increase the quality and efficiency of genomic analyses.

Key Features

Alamut Visual Plus™ integrates genomic information from different curated sources and prediction algorithms in one user-friendly environment.​

This software offers relevant annotations from public databases such as NCBI, EBI, UCSC and is compliant with the HGVS nomenclature. It allows variant reporting with pathogenicity clues from external sources. Functional impact of variants is assessed with relevant prediction tools:​

  • Splicing prediction tools (MaxEntScan, NNSPLICE, GeneSplicer, ESE tools)
  • Missense prediction tools (SIFT, MutationTaster, PolyPhen-2)

Variant reporting is furthermore assisted with semi-automated ACMG/AMP variant classification.​

Alamut Visual Plus™ contains an advanced BAM NGS alignments viewer with VCF support. Sanger electropherograms can also be easily displayed.​

Other Features

  • Automatically connect to the well-curated Alamut software suite database
  • Manage and visualize laboratory’s variants, stored locally or on laboratory local networks.
  • Automatically fill forms in web-based missense prediction tools, eliminating human error risks ​
  • Offer a mutation-focused search engine over PubMed abstracts
  • Cited Variants Reference and link to Mastermind® by Genomenon® ​
  • Compatible with standard bioinformatics file formats (e.g., VCF, BAM, BED)
  • Visualization of different genes in multiple tabs ​
  • Links to external locus-specific databases

Available Annotations

  • Nucleotide conservation (phastCons scores)
  • Reference transcripts
  • dbSNP, gnomAD, ESP/EVS variants ​​
  • Japan Human Genetic Variation Database (HGVD) ​
  • ClinVar pathogenic variants ​
  • COSMIC variants (available at no extra cost to both academic and commercial users — users who wish to download the COSMIC database, manipulate or mine it directly would need to obtain the full data from the Sanger Institute) ​
  • Functional protein domains
  • Protein secondary structure ​
  • Orthologue alignments
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“The [previous] Alamut Visual software was a powerful tool widely used by our teams at CHU of Lille for research decisions in oncogenetics, rare diseases and pharmacogenetics. The new Alamut Visual Plus is a step forward, allowing investigation of deep intronic sequences, the possibility to overlap Sanger sequences with NGS, BAMs and obtain data quickly. Among other features, the variant report is further made easy by including ACMG guidelines.”

Tonio Lovecchio, MSc, Engineer
Cell and Molecular Biology Engineering, CHU of Lille, France

Technical Specifications

OPERATING SYSTEM

The program is available for the following operating systems:

  • Microsoft Windows 10 64-bit version
    The program is available as a binary program (.exe or .zip)
  • MAC OS X (from 10.14 Mojave)
    The program is available as a Disk image (.dmg)

INTERNET CONNECTION

An internet connection is required to connect to Alamut’s database server.
The mean data volume exchanged for one gene is around 200 KB.
The software handles connections through HTTP on port 80 and HTTPS on port 443, optionally through a proxy.

MINIMAL HARDWARE REQUIREMENTS

Computer: 1.5GHz+ – 8GBRAM – 500MB free disk space
Display screen resolution: 1024 x 768 pixels
The software does not alter system directories or the registry. Write permissions are required on the software directory to ensure persistence of application and user parameters.

R&D Collaboration

BRIDGES
In this project, we aim to build a knowledge base that will allow identification of women at high-risk of breast cancer, in particular through comprehensive evaluation of DNA variants in known and suspected breast cancer genes.

Learn more about BRIDGES here.

Discover More

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Webinars

Robust CNV detection using whole exome sequencing for complex cases

Consolidated approach for the interpretation of hereditary cancer variants

In this webinar, we will show how Alamut Visual Plus™ has the computational power to pull data sources together, allowing for a consolidated and consistent approach to genomic variant interpretation in the context of hereditary cancers. In addition, we will give a brief overview of the Mastermind® genomic search engine and how the AI-powered tool reduces turnaround time, increases diagnostic yield and accelerates throughput for genomic variant interpretation.
Watch Now
Robust CNV detection using whole exome sequencing for complex cases

Focusing on what matters most: streamlined secondary and tertiary analyses for clinical exome sequencing

In this session, experts from two clinical research laboratories will share how they successfully analyze exome data using the SOPHiA DDM™ platform and Alamut Visual Plus™. In particular, we will present the results of two recent benchmarking studies for the routine use of clinical exome analyses, that 1) offer evidence to safely discontinue Sanger sequencing as a test to verify the SNVs/Indels detected by NGS and 2) suggest NGS as a first-tier test in the diagnosis of neurodevelopmental disorders.
Watch Now
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Contact our support team

By email:
[email protected]

Support service opening hours (excluding French bank holidays):
09.00-17.00 Mon-Thu, 09.00-16.30 Fri, CET.

Support modalities

Nature of the problem Turnaround time
Malfunction resulting in an interruption of the system in production or severe restrictions on its use, in a prohibitive and non-circumventible manner by the user, and preventing access to data in read or write 4 business hours following notification of incident by email
Dysfunction, the consequences of which do not block degraded use of Alamut Visual Plus™, but causing significant discomfort in its use 2 business days following notification of incident by email
Minimal dysfunction, the consequences of which do not affect the use of Alamut Visual Plus™ or the results provided 5 business days following notification of incident by email

Get in touch

Any questions? Please fill out the form below and select a subject. Your request will be processed ASAP.