alamut

[ah•la•mῡt] - noun

1. the software that redefines the process of mutation interpretation

features

easy-to-use graphical user interface

Click to enlarge

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

documentation

Download alamut brochure.

View alamut documentation.