[ah•la•mῡt] - noun
1. the software that redeﬁnes the process of mutation interpretation
easy-to-use graphical user interface
main features in alamut
- Gene browser over 18,000+ human protein coding nuclear and mitochondrial genes
- Supports NCBI36 and GRCh37 (hg18 and hg19) genome assemblies as well as RefSeqGene and LRG sequences
- Available annotations (as of early 2013): nucleotide conservation (phastCons and phyloP scores), reference transcripts, dbSNP variations with allele frequencies, variants from the NHLBI GO Exome Sequencing Project, HGMD® Professional, SwissProt pathogenic variants, COSMIC mutations, functional protein domains, orthologues
- Calculates theoretical consequences of substitutions, insertions and deletions (effects on protein sequence, frameshifts, splicing effects, miRNA targets, nonsense-mediated mRNA decay)
- Generates mutation reports with full HGVS nomenclature version 2.0, and pathogenicity clues
- Splicing predictions based on 5 different algorithms (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, Human Splicing Finder)
- Automated access to web-based variant scoring algorithms (Align GVGD, SIFT, MutationTaster, PolyPhen-2)
- Import variant annotations from external sources - Variant data exchange through Café Variome – DMuDB export functionality
- Easy access to LOVD locus-specific databases
- Mutation-focused search engine over PubMed abstracts
- Extended and easy access to information by genomic or cDNA position, by identifier, by HGVS variant description or list of variants–the latter is especially convenient for NGS analysis
- Manages and visualizes sequence based private annotations (e.g. primers, probes)
- Visualizes datasets available in standard bioinformatics formats (e.g., BED, GFF)
- Integration of annotations from BIOBASE Genome Trax™
- Automatically connects to Interactive Biosoftware’s regularly updated data servers
- Manages and visualizes lab’s variants
new features in alamut version 2.3.1 (May 2013)
New track with COSMIC somatic variants. Variants can be filtered by tissue and searched by id
- Improved BAM alignment viewer with target visualization, anomalous insert size detection, linear or quadratic coverage histogram, enhanced settings and usability. First and second read counts in paired-end sequencing are now displayed per position on coverage sub-track.
All available transcripts of a gene can now be displayed simultaneously
Customizable visualization of web-based external annotations, including RepeatMasker and DGV
ESP: New coverage and average read depth information. Variant export annotations now include ESP data.
Improved private annotations visualization with full and squish display modes
- LOVD 3.0 search capability in addition to LOVD 2.0
Peptide sequence search in protein sequence
High resolution screen shots
- Embedded web information page
Download alamut brochure.
View alamut documentation.