Alamut® Genova, the reference software for humanvariation exploration
Alamut Genova is a full human genome browser, helping scientists assess the pathogenic status of human alterations. The software integrates genomic information from different curated sources and prediction algorithms in one user-friendly environment.
Alamut Genova offers a unique user interface with relevant annotations gathered 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 (SpliceSiteFinder-like, MaxEntScan, NNSPLICE, GeneSplicer, ESE tools)
- Missense prediction tools (Align GVGD, SIFT, MutationTaster, PolyPhen-2, KD4v)
Variant reporting is furthermore assisted with semi-automated ACMG/AMP variant classification.
Alamut Genova contains an advanced BAM NGS alignments viewer withVCF support. Sanger electropherograms can also be easily displayed in context.Tertiarystructures of a number of proteins, along with variant location, can beinteractively viewed in 3D.
- Automatically connect to the well-curated Alamut software suite database
- Manage and visualize laboratory’s variants, stored locally or on laboratory local networks as well as sequence-based private annotations (e.g. primers, probes)
- Automatically fill forms in web-based missense prediction tools, eliminating human error risks
- Offer a mutation-focused search engine over PubMed abstracts
- Compatible with 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 the full data from the Sanger Institute)
- Functional protein domains
- Protein secondary structure
- Orthologue alignments
- Links to external locus-specific databases