Alamut Visual

Features of Alamut® Visual

Alamut® Visual, the reference software for human variation interpretation

MAIN FEATURES

  • Gene browser supporting human genes (protein coding, non-protein coding and pseudogenes)
  • A single user interface with relevant annotations gathered from public databases such as NCBI, EBI, UCSC
  • HGVS nomenclature compliant software
  • Mutation reporting with pathogenicity clues
  • Calculates functional impact of variants with relevant prediction tools:
    • Splicing prediction tools (SpliceSiteFinder-like, MaxEntScan, NNSPLICE, GeneSplicer, Human Splicing Finder)
    • ESE tools
    • Missense prediction tools (Align GVGD, SIFT, MutationTaster, PolyPhen-2, KD4v)
  • Advanced BAM NGS alignments viewer with VCF support

OTHER FEATURES

  • Automatically connects to the well-curated Alamut software suite database
  • Manages and visualizes lab’s variants
  • Automatic form filling of web-based missense prediction tools
  • Mutation-focused search engine over PubMed abstracts
  • Manages and visualizes sequence-based private annotations (e.g. primers, probes)
  • Uses standard bioinformatics file formats (e.g., VCF, BAM, BED, GFF)

AVAILABLE ANNOTATIONS

  • Nucleotide conservation (phastCons and phyloP scores)
  • Reference transcripts
  • dbSNP, ExAC, ESP/EVS variants
  • Genome of the Netherlands (GoNL), Japan Human Genetic Variation Database (HGVD)
  • ClinVar, SwissProt 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 it from the Sanger Institute)
  • Integrates HGMD® Professional (requires a separate subscription from QIAGEN)
  • Functional protein domains
  • Orthologues alignments
  • Links to external locus-specific databases

 

Alamut Visual complies with the ACMG/AMP Variant Interpretation Standards and Guidelines. Click here for details.

Alamut Visual screenshot



What they say
about Alamut Visual

"We were early Alamut adopters and this software has become essential to our daily diagnosis lab practice, saving time and reducing mistakes. The intuitivity of use and the new functionalities are a very useful help in our daily work."

PASCALE RICHARD M.D. Ph.D.
Paris, France

Events

22.03.2017

ACMG 2017

USA

31.10.2016

Variant Effect Prediction Training Course

Greece