Retained Packaging Signal Interval
Map retained construct sequence to a supplied packaging-signal interval; sequence overlap alone does not establish functional packaging.
Description
Measure overlap between supplied packaging-signal and retained-sequence intervals using zero-based, half-open coordinates.
Packaging signals are sequence features involved in selecting or incorporating a viral genome into a particle. Whether a signal functions can depend on sequence, structure, and surrounding context. Retaining its coordinate span is therefore a geometric check, separate from verifying its biological activity.1
This tool uses zero-based, half-open intervals: the start is included and the end is excluded. The interval [100,200) contains 100 bases, and [200,300) touches it without sharing a base. Both supplied intervals must refer to the same underlying coordinate system.2
Retained Packaging Signal Interval returns overlapping bases, their fraction of the signal span, and whether the entire span lies in the retained interval. It accepts one continuous interval for each input.
When to check retention of a supplied signal span
Use this tool when comparing a retained region with an independently annotated packaging-signal interval. It can expose incomplete coverage or coordinate-convention errors before deeper sequence interpretation.
- Calculate partial or complete overlap with a known interval.
- Check whether touching endpoints imply zero shared bases.
- Document the retained fraction of the supplied signal span.
How to enter intervals and compute retained overlap
- Enter Signal start bp and Signal end bp as nonnegative integer coordinates with end greater than start.
- Enter Retained start bp and Retained end bp using the same reference and half-open convention, also with end greater than start.
- Run the tool and read Retained signal bases, Signal retained fraction, and Complete signal retained.
overlap = max(0, min(signalEnd, retainedEnd) − max(signalStart, retainedStart)); fraction = overlap/(signalEnd − signalStart) The complete-retention flag is true exactly when overlap equals the signal interval length.
The implementation validates safe-integer coordinates and nonempty intervals, then calculates the intersection directly. It does not remap coordinates after deletions, inspect a sequence, or use an overall genome-length bound.
{
"input": {
"signalStartBp": 100,
"signalEndBp": 200,
"retainedStartBp": 150,
"retainedEndBp": 400
},
"output": {
"retainedSignalBases": 50,
"signalRetainedFraction": 0.5,
"completeSignalRetained": false
}
}| Interval relation | Result |
|---|---|
| Retained interval contains the signal | Full signal length, fraction 1, and complete flag true. |
| Disjoint or touching intervals | Zero bases, fraction 0, and complete flag false. |
| Zero-length, reversed, negative, or fractional coordinates | Input error. |
Limitations of coordinate-only signal retention
- Overlap does not establish sequence identity, preserved RNA structure, orientation, or functional packaging.
- Only one contiguous retained interval is represented. Multiple fragments or deletions require separate interval accounting.
- Reference identity and coordinate conversion are the caller’s responsibility. One-based inclusive coordinates must be converted before entry.
- No sequence retrieval, alignment, genome-length validation, or annotation lookup is performed.
Alternative or Complementary interval accounting
Check deletion unions when several removed regions affect retained sequence, and inspect breakpoint assignments against annotated regions when endpoints need classification. These coordinate checks complement sequence and functional evidence rather than establishing packaging competence.
References
-
RNA Structures and Their Role in Selective Genome Packaging — Viruses (2021)
-
Genome Browser FAQ: BED coordinate definitions — University of California, Santa Cruz Genome Browser
Similar or alternative tools
- Defective Genome Deletion Union
Merge overlapping half-open deletions to count removed and retained genome bases.
- Breakpoint Region Overlap
Assign supplied breakpoint positions to named half-open annotation intervals.