Polya Signal Scanner

Find an upstream AAUAAA polyadenylation signal and cleavage-site spacing.

Description

The canonical AAUAAA signal lies upstream of a cleavage position.

The canonical AAUAAA signal lies upstream of a cleavage position. Spacing here is measured from the motif's end rather than its beginning.^[1]

Find an upstream AAUAAA polyadenylation signal and cleavage-site spacing.

When to use Polya Signal Scanner

Use this tool to find an upstream AAUAAA polyadenylation signal and cleavage-site spacing.

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.

How to use Polya Signal Scanner and understand its results

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.
Enter rnaSequence, cleavageIndex, minimumDistance, maximumDistance using the field table and calculation rules, then run the tool.
Read motifStart, distanceToCleavage, withinWindow. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
rnaSequence	RNA sequence	string	Required
cleavageIndex	Cleavage index	number	Required
minimumDistance	Minimum distance	number	Required
maximumDistance	Maximum distance	number	Required

Enter a nonempty nucleotide sequence, zero-based cleavage coordinate within 0 through sequence length and an ordered nonnegative distance window. Uppercase and convert T to U, then choose the last AAUAAA start at or before cleavageIndex−6. Return its zero-based start, spacing and inclusive window flag. No motif is an error.

distance=cleavageIndex−(motifStart+6)

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
motifStart	Motif start	number
distanceToCleavage	Distance to cleavage	number
withinWindow	Within window	boolean

json

{
  "input": {
    "rnaSequence": "AAUAAAACCC",
    "cleavageIndex": 10,
    "minimumDistance": 0,
    "maximumDistance": 20
  },
  "output": {
    "motifStart": 0,
    "distanceToCleavage": 4,
    "withinWindow": true
  }
}

Limitations and assumptions

Only this exact motif is searched. Coordinates are finite numbers without integer enforcement and JavaScript substring rules apply. Very early cleavage indices can select a start-zero motif through lastIndexOf's clamped search position; inspect returned spacing.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Extremely large text inputs are rejected. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors. A successfully returned false flag is an evaluated outcome; its meaning is explained above.

Alternative or Complementary methods

Use Polya Usage Shift: Detect proximal polyadenylation usage shifts between conditions. For a complementary task, use DRACH Motif Density: Scan DRACH motifs and report sites per kilobase of RNA.

References

Polya Signal Scanner — tool.io

Similar or alternative tools

Polya Usage Shift
Detect proximal polyadenylation usage shifts between conditions.
DRACH Motif Density
Scan DRACH motifs and report sites per kilobase of RNA.