Canonical Splice Support
Count canonical GT–AG splice junction motifs.
Description
GT–AG is one common splice-junction motif on a correctly oriented DNA sequence.
GT–AG is one common splice-junction motif on a correctly oriented DNA sequence. Motif tallying differs from validating a junction's alignment and read support.1
Count canonical GT–AG splice junction motifs.
When to use Canonical Splice Support
Use this tool to count canonical GT–AG splice junction motifs.
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 Canonical Splice Support 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 donorMotifs, acceptorMotifs, minimumCanonicalPercent using the field table and calculation rules, then run the tool.
- Read canonicalCount, canonicalPercent, 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 |
|---|---|---|---|
| donorMotifs | Donor motifs | list of string | Required |
| acceptorMotifs | Acceptor motifs | list of string | Required |
| minimumCanonicalPercent | Minimum canonical percent | number | Required |
Enter aligned nonempty motif lists and a finite minimum percentage. Compare exact uppercase two-base strings, count matches and return percentage with an inclusive threshold flag. Whitespace is not trimmed and RNA GU does not match DNA GT.
canonical if uppercase(donor)==GT AND uppercase(acceptor)==AG Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| canonicalCount | Canonical count | number |
| canonicalPercent | Canonical percent | number |
| passes | Passes | boolean |
{
"input": {
"donorMotifs": [
"GT",
"GC",
"GT"
],
"acceptorMotifs": [
"AG",
"AG",
"AC"
],
"minimumCanonicalPercent": 50
},
"output": {
"canonicalCount": 1,
"canonicalPercent": 33.33333333333333,
"passes": false
}
}Limitations and assumptions
Other motif strings are counted as noncanonical rather than rejected. Strand orientation, genome coordinates, minor canonical motifs and read-quality support are not analyzed.
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. A successfully returned false flag is an evaluated outcome; its meaning is explained above.
Alternative or Complementary methods
Use Junction Annotation Tally: Tally annotated versus novel observed splice junctions. For a complementary task, use Strand Specificity: Check library strandedness using sense-versus-antisense reads.
References
-
Canonical Splice Support — tool.io
Similar or alternative tools
- Junction Annotation Tally
Tally annotated versus novel observed splice junctions.
- Strand Specificity
Check library strandedness using sense-versus-antisense reads.