Alamut Visual is a gene browser supporting human genes (protein coding, non-protein coding and pseudogenes).
It offers a single user interface with relevant annotations gathered from public databases such as NCBI, EBI, UCSC and is compliant with HGVS nomenclature. It allows variants reporting with pathogenicity clues from external sources. Functional impact of variants is assessed by the biologist with relevant prediction tools:
- Splicing prediction tools (SpliceSiteFinder-like, MaxEntScan, NNSPLICE, GeneSplicer)
- ESE tools
- Missense prediction tools (Align GVGD, SIFT, MutationTaster, PolyPhen-2, KD4v)
Alamut Visual contains an advanced BAM NGS alignments viewer with VCF support.
- Alamut Visual automatically connects to the well-curated Alamut software suite database
- It manages and visualizes lab’s variants
- It automatically fills in web-based missense prediction tools forms, eliminating human error risks
- It contains a mutation-focused search engine over PubMed abstracts
- Alamut Visual manages and visualizes sequence-based private annotations (e.g. primers, probes)
- It uses standard bioinformatics file formats (e.g., VCF, BAM, BED, GFF)
- 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, 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)
- 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.