miRNA Seed Matcher

Locate reverse-complementary miRNA seed matches in a target RNA.

Description

A miRNA seed can pair with its reverse complement in a target RNA.

A miRNA seed can pair with its reverse complement in a target RNA. Exact seed matches are sequence candidates rather than predictions of functional repression.^[1]

Locate reverse-complementary miRNA seed matches in a target RNA.

When to use miRNA Seed Matcher

Use this tool to locate reverse-complementary miRNA seed matches in a target 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 miRNA Seed Matcher 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 mirna, targetRna, seedStart, seedLength using the field table and calculation rules, then run the tool.
Read seed, reverseComplement, matchPositions. 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
mirna	miRNA	string	Required
targetRna	Target rna	string	Required
seedStart	Seed start	number	Required
seedLength	Seed length	number	Required

Enter nonempty RNA-only A/C/G/U sequences, a seed start of at least one and positive length that fits the miRNA. Uppercase both, extract the seed, reverse-complement it and scan every target position. Return seed, reverse complement and zero-based positions, including overlaps. Use integer seed coordinates; the runtime does not enforce integrality.

seed=miRNA slice from one-based start; matches=all exact target occurrences of reverseComplement(seed)

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

Output field	Meaning	Value type
seed	Seed	string
reverseComplement	Reverse complement	string
matchPositions	Match positions	list of number

json

{
  "input": {
    "mirna": "AUGCUAAA",
    "targetRna": "AAAAGCAUCCC",
    "seedStart": 2,
    "seedLength": 7
  },
  "output": {
    "seed": "UGCUAAA",
    "reverseComplement": "UUUAGCA",
    "matchPositions": []
  }
}

Limitations and assumptions

T bases, gaps and ambiguous symbols are rejected. Accessibility, mismatches, binding energy and off-target databases are not 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.

Alternative or Complementary methods

Use siRNA GC Screen: Screen siRNA GC percentage against user-selected design bounds. For a complementary task, use Probe Off Target Filter: Filter array probes by caller-supplied best off-target sequence identity.

References

miRNA Seed Matcher — tool.io

Similar or alternative tools

siRNA GC Screen
Screen siRNA GC percentage against user-selected design bounds.
Probe Off Target Filter
Filter array probes by caller-supplied best off-target sequence identity.