Abstract
Autosomal recessive spastic ataxia of Charlevoix–Saguenay is a distinct form of hereditary early-onset spastic ataxia caused by cerebellum and spinal cord degeneration. The SACS gene has been demonstrated to be responsible for the disease through worldwide description of different mutations. We report here a computational analysis of a novel SACS gene mutation identified in a Tunisian family, using workflow implemented on the BioExtract Server. Several online computational tools are currently available to explore the effect of novel identified mutations in human and other organisms. Such analysis is time-consuming and generates a batch of files that researchers need to extract and save. The BioExtract Server workflow described here offers an easy way to execute the required tools together, avoiding entering queries independently in each web tool or service.
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Acknowledgments
The authors would like to thank Dr. Volker Brendel for the helpful comments and suggestions on the earlier versions of their manuscript.
Funding
The BioExtract Server is funded through the National Science Foundation grant: DBI-0606906. V. Brendel, PI, C. Lushbough (U. South Dakota), and Carolyn Lawrence (ARS-USDA), co-PIs; Cyberinfrastructure for (Comparative) Plant Genome Research through PlantGDB.
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Supplemental material 1
Supermatcher tool result showing the p.D4464Y substitution. (DOC 457 kb)
Supplemental material 2
Multiple alignment result showing that the D residue is highly conserved within species (DOC 602 kb)
Supplemental material 3
Pepstat analysis results: replacement of a polar residue in the wild-type protein (right) by a nonpolar one in the mutated protein (left). (DOC 422 kb)
Supplemental material 4
The predicted effect of p.D4464Y substitution on the secondary structure using GOR method. (DOC 420 kb)
Supplemental material 5
Hmoment analysis results showing modifications in the hydrophobic moment between the wild-type and the mutated protein (highlighted region). (DOC 115 kb)
Supplemental material 6
Comparison of hydrophobicity between the wild-type (left) and the mutated (right) protein with pep info tool using Kyte & Doolittle, OHM, and consensus parameters. Kyte & Doolittle methods do not predict any obvious change between the two plots, whereas hydrophobicity decreasing could be observed by the two remaining methods between residues 4450 and 4470. (DOC 1343 kb)
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Bouhlal, Y., Jennewein, D.M., Anderson, B. et al. Computational Analysis of a Novel SACS Gene Mutation with BioExtract Server. J Mol Neurosci 44, 53–58 (2011). https://doi.org/10.1007/s12031-011-9512-8
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DOI: https://doi.org/10.1007/s12031-011-9512-8