AlamutVisual

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
  • Integrates HGMD® Professional and Genome Trax™ (requires separate subscriptions from QIAGEN)
  • Functional protein domains
  • Orthologues alignments
  • Links to external locus-specific databases

image

What they say
about Alamut Visual

"We have found Alamut to be an immensely useful tool, and would recommend Alamut to anyone looking for a powerful yet straightforward software program that is able to accurately catalogue and evaluate mutations."

JOHN GARCIA, Invitae
San Francisco, USA

Events

07.10.2015

ASHG 2015

USA

06.06.2015

ESHG 2015

United Kingdom