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[…] ted out SNVs called with variant reads ≥95% as homozygous and SNVs with variant reads ≥30% to ≤70% as heterozygous ones. Reads with variants ≤5% were removed from the account. Rest of the variant calls (5% to <30%, >70% to <95%) were considered ambiguous, and they were not used for plotting. Chromosome wise plotting of the data was carried out using R-project., In order to understand the possible consequences of the frameshift deletion on the 3-dimensional structure of the protein, we generated protein model of the wild-type and mutant CNGB3 protein. Because of the low sequence identity between CNGB3 and template PDBID: 5K7L (20%), we used secondary structure-based threading server PHYRE[] to generate the CNGB3 model, taking the Eag1 crystal structure (PDB ID: 5K7L chain A) as a template. All sequence similarity searches were carried out in the MPI Bioinformatics Toolkit using HHpred[] with default settings. HHpred searches for template were performed against a database comprising PDB70 (protein databank structures, as available on January 19, 2017) clustered at 70% sequence identity. Chimera tool was used for visualization and analysis of the modeled protein structure.[], In the recruited family (Fig. A), 3 of the 6 siblings had complaints of poor visual acuity, photophobia, and disturbed color vision since early childhood. Fundus examination disclosed vascular attenuation and macular RPE changes in all the affected siblings, signifying degeneration of photoreceptor cells (Fig. B). The index patient III.5 was investigated initially at the age of 9 years, with complaints of poor vision and photo […]

Pipeline specifications

Software tools Phyre, MPI Bioinformatics Toolkit, HHPred
Diseases Disease, Wiskott-Aldrich Syndrome, Photophobia, Precursor Cell Lymphoblastic Leukemia-Lymphoma, Retinal Dystrophies
Chemicals Nucleotides