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Reference: Bao L., Cui Y. nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms. Nucleic Acids Research (2005) 33 W480-W482.
Hosted: Developed and maintained by Yan Cui’s lab at the University of Tennessee, Health Science Center. (http://snpanalyzer.uthsc.edu/)

Summary:
nsSNPAnalyzer integrates information from multiple sequence alignments and protein structure to identify disease-associated variants using a random forest method.

Methodology:
• If not provided, a homologous protein structure is obtained from the ASTRAL database. From this, the solvent accessibility (how buried the site is), polarity and secondary structure of the substitution site is determined.
• An alignment is generated and SIFT predictions are made.
• These feed into a random forest predictor, trained on a known data.
• If no structural homologue is found, no prediction can be given.

Input:
The user must provide a protein sequence, either uploaded or pasted, in FASTA format. The substitutions must be provided and the user has the option to also provide a PDB file.