Alamut Visual Plus

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 (Align GVGD, 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 and phyloP scores) ​
  • Reference transcripts ​
  • dbSNP, gnomAD, ESP/EVS variants ​
  • Genome of the Netherlands (GoNL), Japan Human Genetic Variation Database (HGVD) ​
  • ClinVar, UniProt 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

What they say
about Alamut

"In developing new genetic assays and evaluating the implications of newly identified sequence variations, Alamut helps me work faster and safer to ensure and document quality in assay design and interpretations."

Oslo University Hospital, Norway