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Fig. 1 | Genome Biology

Fig. 1

From: In silico methods for predicting functional synonymous variants

Fig. 1

Workflow schematic for how to optimally use in silico tools to investigate synonymous variants. Genetic sequences containing synonymous variants can cause many different functional effects, including alterations to codon usage biases, mRNA structure, splicing, miRNA binding, disease pathogenesis, and protein characteristics. After (1) identifying a functional mechanism of interest, (2) a variety of different in silico tools can be chosen and applied to evaluate the sequence containing synonymous variants. After the sequence has been processed, (3) outputs of these tools can be analyzed to form predictions. For proper evaluation, most tools will require input of a short nucleotide sequence containing the synonymous variant. The wild-type sequence for the identical region encompassing the synonymous variant should be processed for comparison. Examples of potential outputs for tools highlighted in row 2 are shown in row 3. CodonStatsDB determines codon preferences based on RSCU values. UNAFold can generate predicted mRNA structures and calculate differences in mRNA stability. NNSplice will reveal any new or lost splice sites. Paccmit-CDS is able to capture changes to miRNA binding sites. usDSM is able to predict the pathogenicity of the variant. Outputs may vary depending on the algorithms and structure of the tools. It is highly beneficial to analyze the sequence through multiple tools and to validate the results through experimental methods

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