DRACH Motif Density

Scan DRACH motifs and report sites per kilobase of RNA.

Description

DRACH is a degenerate five-base motif often used to enumerate candidate RNA sequence contexts.

DRACH is a degenerate five-base motif often used to enumerate candidate RNA sequence contexts. Motif presence alone does not demonstrate a chemical modification.^[1]

Scan DRACH motifs and report sites per kilobase of RNA.

When to use DRACH Motif Density

Use this tool to scan DRACH motifs and report sites per kilobase of RNA.

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 DRACH Motif Density 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, minimumMotifsPerKb using the field table and calculation rules, then run the tool.
Read motifStarts, motifsPerKb, passes. 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
minimumMotifsPerKb	Minimum motifs per kb	number	Required

Enter nonempty A/C/G/T/U text and a finite minimum density. Uppercase and convert T to U, scan every five-base window including overlaps and return zero-based motif starts, sites per kb and an inclusive density flag. Shorter sequences have zero sites.

DRACH=[A/G/U][A/G]AC[A/C/U]; density=1000 motifCount/sequenceLength

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

Output field	Meaning	Value type
motifStarts	Motif starts	list of number
motifsPerKb	Motifs per kb	number
passes	Passes	boolean

json

{
  "input": {
    "rnaSequence": "GGACUAAAGGACU",
    "minimumMotifsPerKb": 100
  },
  "output": {
    "motifStarts": [
      0,
      8
    ],
    "motifsPerKb": 153.84615384615387,
    "passes": true
  }
}

Limitations and assumptions

Ambiguous bases and whitespace are rejected. No modification measurement, site probability, structural accessibility or transcript annotation is evaluated.

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 Signal Scanner: Find an upstream AAUAAA polyadenylation signal and cleavage-site spacing. For a complementary task, use miRNA Seed Matcher: Locate reverse-complementary miRNA seed matches in a target RNA.

References

DRACH Motif Density — tool.io

Similar or alternative tools

Polya Signal Scanner
Find an upstream AAUAAA polyadenylation signal and cleavage-site spacing.
miRNA Seed Matcher
Locate reverse-complementary miRNA seed matches in a target RNA.