Description
Return k-mer windows lost by clipping sequence ends.
Computational biology distinguishes discrete counts, probabilistic weights, sequence indexes and logical rules. A supplied event or record flag can be summarized without simulating a stochastic process, validating a sequence annotation or establishing a biological mechanism.
Return k-mer windows lost by clipping sequence ends.
When to use this tool
Use Sequence Kmer Edge Loss when checking the stated count, sequence, Boolean-rule or support convention.
How to use the tool and how it works
- Enter sequenceLength, k, clippedLeft, clippedRight. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read originalWindows, retainedWindows, lostWindows. Use the output convention below.
Return k-mer windows lost by clipping sequence ends. Require whole length >= 0, k >= 1 and nonoverlapping left/right clips; windows = max(0,length-k+1), retained uses clipped length and lost subtracts.1
| Input field | Meaning and units | Accepted input |
|---|---|---|
| sequenceLength | Sequence Length | Required. Safe integer; minimum 0. |
| k | K | Required. Safe integer; minimum 1. |
| clippedLeft | Clipped Left | Required. Safe integer; minimum 0. |
| clippedRight | Clipped Right | Required. Safe integer; minimum 0. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| originalWindows | Original Windows | Required. Safe integer. |
| retainedWindows | Retained Windows | Required. Safe integer. |
| lostWindows | Lost Windows | Required. Safe integer. |
{
"input": {
"sequenceLength": 10,
"k": 3,
"clippedLeft": 1,
"clippedRight": 2
},
"output": {
"originalWindows": 8,
"retainedWindows": 5,
"lostWindows": 3
}
}Limitations and assumptions
- This counts contiguous windows only; no sequence content, alphabet, read quality or k-mer uniqueness is inspected.
- 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 complete sequence, identifier universe or stochastic/logical model for actual inference, sampling and uncertainty analysis.
References
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