Alamut Batch

Features of Alamut® Batch

Alamut Batch offers numerous features and dozens of annotations for the NGS analysis of your variants

MAIN FEATURES

Alamut Batch is an efficient high-throughput human variant annotation engine for large studies like NGS analysis.
The annotation engine supports human genes (protein coding, non-protein coding and pseudogenes).
The data enrichment is based on the well-curated Alamut® software Suite database and on efficient prediction tools.
Alamut Batch is easy to integrate into any analysis pipeline (Linux, Windows).
It uses standard bioinformatics file formats (e.g. tab-delimited, VCF).

OTHER FEATURES

The annotations can be restricted/limited to user-defined regions. The external annotations supplied in variant annotation files can be integrated in the output.
Alamut Batch integrates annotations from HGMD® Professional* (BIOBASE).
A GUI frontend is available on Windows.
Alamut Batch is available as a client-server or standalone application (including the Alamut® database).

AVAILABLE ANNOTATIONS

Variant location, type, coding effects, HGVS nomenclature

  • Gene: symbol, HGNC id, OMIM® id
  • Transcripts: RefSeq id, strand, length
  • Protein: RefSeq id, Uniprot id, domains
  • Variant type: substitution, deletion, insertion, duplication, delins
  • Coding effect: synonymous, missense, nonsense, in-frame, frameshift, start loss, stop loss
  • Variant location: upstream, 5’UTR, exon, intron, 3’UTR, downstream
  • gDNA-level, cDNA-level, protein-level HGVS nomenclature
  • Exon and/or intron number

Identification with variation databases

  • dbSNP, ExAC, ESP/EVS
  • ClinVar, SwissProt
  • COSMIC (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)
  • HGMD® Professional (requires separate subscription from QIAGEN)

Splicing predictions

  • MaxEntScan, NNSPLICE, Human Splicing Finder, SpliceSiteFinder, GeneSplicer predictions
  • Effect on nearest natural splice site
  • Splicing effect in variation vicinity (e.g. new splice site, activation of nearby cryptic site)
  • Branch point predictions

Missense annotations and predictions

  • phastCons and phyloP nucleotide conservation scores
  • Codon detailed annotations
  • Amino acid conservation in orthologues
  • BLOSUM scores, Grantham distance, amino acid physico-chemical features
  • Growing list of missense prediction tools: SIFT, Align GVGD, MAPP


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

17.10.2017

ASHG 2017

USA

27.05.2017

ESHG 2017

Denmark