Description
Return CDS phase carry and strand-end convention.
Genome annotations depend on coordinate origin, endpoint inclusion, strand and reading-phase conventions. A local offset or phase token can be handled precisely while a complete transcript, reference identity and biological reading frame remain separate validation questions.
Return CDS phase carry and strand-end convention.
When to use this tool
Use GFF3 Phase Strand Carry when checking the stated genomic coordinate, annotation phase or attribute-value convention.
How to use the tool and how it works
- Enter featureLength, phase, strand. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read nextPhase, phaseAt. Use the output convention below.
Return CDS phase carry and strand-end convention. Require positive whole featureLength, phase 0..2 no greater than length and strand plus/minus; nextPhase = (3-((length-phase) mod 3)) mod 3, phaseAt is start for plus and end for minus.1
Annotation frame/phase fields describe codon offsets under a strand-aware feature convention. A local token or carry calculation does not validate a transcript or translate its sequence.2
| Input field | Meaning and units | Accepted input |
|---|---|---|
| featureLength | Feature Length | Required. Safe integer; minimum 1. |
| phase | 0, 1 or 2 bases skipped from the strand-specific feature beginning before the next complete codon. | Required. Safe integer; minimum 0; maximum 2. |
| strand | Strand | Required. Text; one of "+", "-"; maximum UTF-16 length 8192. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| nextPhase | Next Phase | Required. Safe integer. |
| phaseAt | Phase At | Required. Text; maximum UTF-16 length 8192. |
{
"input": {
"featureLength": 10,
"phase": 0,
"strand": "+"
},
"output": {
"nextPhase": 2,
"phaseAt": "start"
}
}Limitations and assumptions
- This is local phase arithmetic, not validation of a complete transcript, splicing, reference sequence or translated protein.
- Inputs must satisfy both the field types and the cross-field conditions above. Invalid input causes an error; a successful false flag or documented placeholder is a different result.
- Numeric calculations use binary floating point unless exact decimal-integer arithmetic is explicitly stated. No hidden measurement tolerance or decimal rounding is added; nonfinite or out-of-contract results are rejected. Numeric signed-zero results are exported as zero.
Alternative or Complementary methods
Use the intended complete BED/GFF/GTF format, reference assembly and transcript model to validate full annotations and biological meaning.
References
Similar or alternative tools
- Bioinformatics: GFF Phase Token Check
Parse one GFF phase token.
- SAM CIGAR Zero Length Flag Tool
Flag zero-length operations in a supplied parsed CIGAR stream; no alignment or sequence is reconstructed.