Alamut Batch has 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).
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).
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)
- 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