Probe Off Target Filter

Filter array probes by caller-supplied best off-target sequence identity.

Description

Off-target identity screening uses sequence-search results to filter candidate probes.

Off-target identity screening uses sequence-search results to filter candidate probes. The identity threshold and comparison sequences determine what the screen can detect.^[1]

Filter array probes by caller-supplied best off-target sequence identity.

When to use Probe Off Target Filter

Use this tool to filter array probes by caller-supplied best off-target sequence identity.

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 Probe Off Target Filter 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 probeIds, bestOffTargetIdentityPercents, maximumOffTargetIdentityPercent using the field table and calculation rules, then run the tool.
Read retainedProbeIds, filteredProbeIds. 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
probeIds	Probe ids	list of string	Required
bestOffTargetIdentityPercents	Best off target identity percents	list of number	Required
maximumOffTargetIdentityPercent	Maximum off target identity percent	number	Required

Enter aligned nonempty probe IDs and best off-target identities in 0–100, with a finite maximum criterion. Partition IDs using the strict retained and inclusive filtered comparisons, preserving input order.

retain if bestOffTargetIdentity<maximum; filter if identity≥maximum

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

Output field	Meaning	Value type
retainedProbeIds	Retained probe ids	list of string
filteredProbeIds	Filtered probe ids	list of string

json

{
  "input": {
    "probeIds": [
      "a",
      "b",
      "c"
    ],
    "bestOffTargetIdentityPercents": [
      40,
      95,
      70
    ],
    "maximumOffTargetIdentityPercent": 80
  },
  "output": {
    "retainedProbeIds": [
      "a",
      "c"
    ],
    "filteredProbeIds": [
      "b"
    ]
  }
}

Limitations and assumptions

No sequence search or hybridization model is run. Equality is filtered; the criterion is not separately constrained to 0–100, and repeated IDs remain repeated.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. 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 miRNA Seed Matcher: Locate reverse-complementary miRNA seed matches in a target RNA.

References

Probe Off Target Filter — tool.io

Similar or alternative tools

siRNA GC Screen
Screen siRNA GC percentage against user-selected design bounds.
miRNA Seed Matcher
Locate reverse-complementary miRNA seed matches in a target RNA.