Table of Contents : In silico predictions :
Missense predictions | Splicing module | Micro-RNA predictions

Automatically computed missense predictions


InformationAutomatically computed missense predictions done by Align GVGD and SIFT, in Alamut Visual, are based on orthologues alignments. With the new genome build GRCh38 available in Alamut Visual,some orthologues alignments coming from ENSEMBL Compara have been updated and may lead to different predictions that those described for the same genes/transcripts for GRCh37.

Alamut® Visual 2.0 introduced automatically computed missense predictions, while still retaining the ability to query prediction sites manually, giving users the opportunity to adjust prediction settings and options.

Currently, automatically computed predictions are provided for Align GVGD, SIFT and MutationTaster.

Automatically computed predictions are available in the variant window and in variant export data.

InformationThe click buttons enable also to automatically fill in the predictors forms.

This section describes how automatically computed missense predictions are provided in Alamut® Visual.

Align GVGD

Align GVGD predictions are computed using the orthologue alignment provided by Alamut® Visual for the gene under study. See also Orthologue Alignments.

Align GVGD scores interpretation: here.

Current version for precomputed predictions: Align GVGD Tavtigian et al. (2006)

SIFT

SIFT predictions are computed using the orthologue alignment provided by Alamut® Visual for the gene under study. See SIFT Aligned Sequences.

SIFT scores interpretation: here.

Current version for precomputed predictions: SIFT 4.0.3

MutationTaster

MutationTaster predictions are computed using the mapping between NCBI RefSeq and Ensembl Transcript Ids available in Alamut® Visual.

MutationTaster scores interpretation: here.

InformationMutationTaster automatic predictions can be activated or deactivated with the Options dialog box (menu 'Tools' > 'Options' > 'Display' tab).

Current version for precomputed predictions: MutationTaster2 from MutationTaster website

PolyPhen-2

The PolyPhen-2 automatic predictions are not available due to licencing reasons (March 2013).

You can query the prediction site with an automatically filled web form by clicking on "PolyPhen-2..." button.

References

NGRL Manchester Multiple sequence alignment use in missense prediction tools

Tavtigian SV, Deffenbaugh AM, Yin L, Judkins T, Scholl T, Samollow PB, de Silva D, Zharkikh A, Thomas A. Comprehensive statistical study of 452 BRCA1 missense substitutions with classification of eight recurrent substitutions as neutral. J Med Genet. 2005 Jul 13

Ng PC, Henikoff S. Predicting Deleterious Amino Acid Substitutions. Genome Res. 2001 May;11(5):863-74. PubMed

Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense variants. Nat Methods 7(4):248-249 (2010)

Schwarz JM, Rödelsperger C, Schuelke M, Seelow D. MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods. 2010 Aug;7(8):575-6.

Acknowledgments

Special thanks to the Genetic Cancer Susceptibility Group at IARC for their kind help in implementing the Align GVGD algorithm.


© 2018 Interactive Biosoftware - Last modified: 30 December 2017