Users do not have direct access to the Alamut™ Visual Plus database and thus do not need to write...
Do users need access to the SQL database to use Alamut™ Visual Plus?
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FAQs
How is nonsense-mediated mRNA decay (NMD) prediction determined?
In AlamutTM Visual Plus, the limit fixed to trigger NMD is 53 nucleotides.
How frequently do we update each catalog?
Catalogs are updated at the same frequency as the release of those catalogs. For example, Clinvar...
Why is there a difference in nucleotide conservation scores between Alamut Visual and Alamut™ Visual Plus?
Alamut Visual uses conservation scores from UCSC:...
Why are there differences in the species used for conservation between genome builds 37 and 38? This makes the significance of the region look very different. Is there not a specific combination of species that you use as standard? Do these alignments feed into the predictions that are automatically computed?
The Orthologue Alignments for each gene are downloaded from Ensembl Compara...
Why are there differences in SIFT scores between Alamut Visual and Alamut™ Visual Plus?
In Alamut Visual and AlamutTM Visual Plus, the SIFT missense predictors are computed using the...
Why do SIFT scores differ when generated automatically versus manually?
SIFT scores are calculated based on multiple sequence alignments of protein orthologues (SIFT...
Why do Polyphen-2 prediction scores differ when generated automatically versus manually?
The Polyphen-2 prediction scores automatically displayed in AlamutTM Visual Plus are extracted...
Why are there inconsistencies in scores between versions of Polyphen-2?
The following page explains possible reasons for inconsistencies between versions:...
What versions of missense prediction tools are available in Alamut™ Visual Plus?
SIFT 6.2.0Polyphen2
How are SIFT, and other missense prediction scores calculated?
SIFT scores are calculated based on multiple sequence alignments of protein orthologues (SIFT...
Why does the gene SHANK3 not show transcript NM_033517.1?
SHANK3 is quite a problematic gene. AlamutTM Visual Plus mapped the available transcripts to...