lncRNA Coding Potential Gate

Gate a supplied lncRNA coding-potential probability.

Description

A supplied coding-potential score can be compared with a noncoding cutoff.

A supplied coding-potential score can be compared with a noncoding cutoff. The result is a threshold decision on an upstream score rather than sequence-based prediction.^[1]

Gate a supplied lncRNA coding-potential probability.

When to use lncRNA Coding Potential Gate

Use this tool to gate a supplied lncRNA coding-potential probability.

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 lncRNA Coding Potential Gate 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 codingPotential, maximumNoncodingScore using the field table and calculation rules, then run the tool.
Read nonCoding, scoreMargin. 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
codingPotential	Coding potential	number	Required
maximumNoncodingScore	Maximum noncoding score	number	Required

Enter coding probability and maximum noncoding score both in 0–1. Return an inclusive nonCoding flag and signed margin. Equality passes with zero margin.

nonCoding=(score≤cutoff); margin=cutoff−score

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

Output field	Meaning	Value type
nonCoding	Non coding	boolean
scoreMargin	Score margin	number

json

{
  "input": {
    "codingPotential": 0.2,
    "maximumNoncodingScore": 0.4
  },
  "output": {
    "nonCoding": true,
    "scoreMargin": 0.2
  }
}

Limitations and assumptions

No coding model, ORF scan or annotation analysis is run. Score calibration and the threshold's scientific suitability must be established upstream.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. 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 Longest ORF: Find the longest complete start-to-stop ORF and its protein length. For a complementary task, use Utr Length Ratio: Compare 3-prime and 5-prime UTR lengths.

References

lncRNA Coding Potential Gate — tool.io

Similar or alternative tools

Longest ORF
Find the longest complete start-to-stop ORF and its protein length.
Utr Length Ratio
Compare 3-prime and 5-prime UTR lengths.