VarCon

VarCon converts positional information from single nucleotide variation (SNV) annotations and retrieves genomic reference sequences surrounding SNV positions to assess splicing regulatory impacts.

Key Features:

• SNV Position Conversion: Converts positional information from SNV annotations referring to either the coding sequence or the reference genomic sequence.
• Genomic Sequence Retrieval: Retrieves the genomic reference sequence around the position of the single nucleotide variation.
• HEXplorer Score Calculation: Calculates the HEXplorer score as an estimation of whether the SNV could potentially influence binding of splicing regulatory proteins.
• Splice Site Strength Reporting: Reports splice site strengths of splice sites within the retrieved genomic sequence and any changes due to the SNV.

Scientific Applications:

• Splicing Regulatory Impact Assessment: Evaluates whether SNVs may affect binding of splicing regulatory proteins through HEXplorer score estimation.
• Splice Site Analysis: Identifies and quantifies splice site strength alterations caused by SNVs within retrieved genomic contexts.

Methodology:

VarCon converts SNV positional annotations to genomic coordinates, retrieves surrounding reference sequence, calculates HEXplorer scores for splicing regulatory protein binding assessment, and computes splice site strengths for sites within the retrieved sequence.