Alamut Visual Plus™
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.
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
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
“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
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
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
Webinars
Consolidated approach for the interpretation of hereditary cancer variants
Focusing on what matters most: streamlined secondary and tertiary analyses for clinical exome sequencing
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
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