Interface AlternativeSplicingOptions

Options for configuring alternative splicing behavior.

interface AlternativeSplicingOptions {
    allowSkipFirstExon?: boolean;
    allowSkipLastExon?: boolean;
    minimumExonCount?: number;
    requireMinimumExons?: boolean;
    validateCodons?: boolean;
    validateReadingFrames?: boolean;
}

Properties

allowSkipFirstExon? allowSkipLastExon? minimumExonCount? requireMinimumExons? validateCodons? validateReadingFrames?

Properties

Optional Readonly allowSkipFirstExon

allowSkipFirstExon?: boolean

Whether to allow variants that skip the first exon

Optional Readonly allowSkipLastExon

allowSkipLastExon?: boolean

Whether to allow variants that skip the last exon.

Biologically relevant for:

  • Alternative polyadenylation (early termination with different 3' UTR)
  • Nonsense-mediated decay escape mechanisms
  • Research into truncated polypeptide isoforms

When false, enforces that functional polypeptides retain proper C-terminus and termination signals. Use true for modeling alternative polyadenylation or studying naturally occurring truncated isoforms.

Optional Readonly minimumExonCount

minimumExonCount?: number

Minimum number of exons required per variant

Optional Readonly requireMinimumExons

requireMinimumExons?: boolean

Whether to require at least one exon in each variant

Optional Readonly validateCodons

validateCodons?: boolean

Whether to validate that variants maintain proper start/stop codons.

When true, validates:

  • Start codon (AUG) at the beginning of the coding sequence
  • Stop codon (UAA, UAG, UGA) at the end of the coding sequence

Use false for research on partial sequences, alternative start sites, or when studying nonsense mutations with premature stops.

Optional Readonly validateReadingFrames

validateReadingFrames?: boolean

Whether to validate reading frames for each variant

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allowSkipFirstExonallowSkipLastExonminimumExonCountrequireMinimumExonsvalidateCodonsvalidateReadingFrames