siRNA GC Screen

Screen siRNA GC percentage against user-selected design bounds.

Description

GC percentage is one sequence-composition screen for an siRNA design.

GC percentage is one sequence-composition screen for an siRNA design. Passing a caller range does not establish targeting, potency or specificity.^[1]

Screen siRNA GC percentage against user-selected design bounds.

When to use siRNA GC Screen

Use this tool to screen siRNA GC percentage against user-selected design bounds.

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 siRNA GC Screen 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 sirna, minimumGcPercent, maximumGcPercent using the field table and calculation rules, then run the tool.
Read gcPercent, withinRange. 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
sirna	siRNA	string	Required
minimumGcPercent	Minimum gc percent	number	Required
maximumGcPercent	Maximum gc percent	number	Required

Enter nonempty A/C/G/T/U sequence text without whitespace and ordered finite percentage bounds. Uppercase and convert U to T for checking, count G/C and compare inclusively with the supplied bounds. Bound values are not otherwise constrained to 0–100.

GC%=100 numberOfGandC/sequenceLength

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

Output field	Meaning	Value type
gcPercent	Gc percent	number
withinRange	Within range	boolean

json

{
  "input": {
    "sirna": "GCGCAATT",
    "minimumGcPercent": 30,
    "maximumGcPercent": 60
  },
  "output": {
    "gcPercent": 50,
    "withinRange": true
  }
}

Limitations and assumptions

Ambiguous bases and annotations are rejected. No sequence-length design rule, off-target search, duplex thermodynamics or experimental activity prediction is included.

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 miRNA Seed Matcher: Locate reverse-complementary miRNA seed matches in a target RNA. For a complementary task, use Gapmer Layout: Assemble and assess an antisense wing-gap-wing oligonucleotide layout.

References

siRNA GC Screen — tool.io

Similar or alternative tools

miRNA Seed Matcher
Locate reverse-complementary miRNA seed matches in a target RNA.
Gapmer Layout
Assemble and assess an antisense wing-gap-wing oligonucleotide layout.