Paralog Age Peaks

Detect strict interior peaks in a supplied paralog-age histogram as candidate duplication signals.

Description

A paralog-age histogram can contain peaks suggestive of duplication history.

A paralog-age histogram can contain peaks suggestive of duplication history. Local maxima identify candidate signals that need further biological analysis.

Detect strict interior peaks in a supplied paralog-age histogram as candidate duplication signals.

When to use Paralog Age Peaks

Use this for the following task: Detect strict interior peaks in a supplied paralog-age histogram as candidate duplication signals.

Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.

How to use Paralog Age Peaks and understand its results

Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
Enter binCenters, paralogCounts, minimumPeakCount using the field table, then run the tool.
Read peakCenters, peakCounts. Interpret flags, units, ordering and placeholder values using the rules below.
Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.

Input field	Meaning	Value type and bounds	Requirement
binCenters	Bin centers	list of number; minimum entries 3; maximum entries 100000; each entry: number; minimum 0	Required
paralogCounts	Paralog counts	list of integer; minimum entries 3; maximum entries 100000; each entry: integer; minimum 0	Required
minimumPeakCount	Minimum peak count	integer; minimum 1	Required

Align strictly increasing bin centers with counts. Examine interior bins only and preserve their order in the returned peaks.^[1]

peak at i when count[i] ≥ minimum AND count[i] > both adjacent counts

This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.

Output field	Meaning	Value type
peakCenters	Strict interior maxima above both neighbors and at least minimumPeakCount; edges and plateaus are excluded.	list of number
peakCounts	Peak counts	list of integer

json

{
  "input": {
    "binCenters": [
      0.1,
      0.2,
      0.3,
      0.4,
      0.5
    ],
    "paralogCounts": [
      1,
      5,
      2,
      6,
      1
    ],
    "minimumPeakCount": 4
  },
  "output": {
    "peakCenters": [
      0.2,
      0.4
    ],
    "peakCounts": [
      5,
      6
    ]
  }
}

Limitations and assumptions

Endpoints and flat plateaus are not peaks here. Ages, binning and duplication interpretation are supplied externally.

The tool operates on supplied local data; alignment, filtering and annotation must already be appropriate for the stated calculation. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.

Alternative or Complementary methods

Choose Synonymous Clock Divergence for this operation: Estimate divergence time from dS assuming equal constant substitution rates on both lineages. For a complementary task, use Reciprocal Best Hit Pairs for this operation: Validate reciprocal best-hit gene pairs from independently supplied forward and reverse maps.

The implementation reference documents the exact calculation, supported input shapes and returned fields.

References

Paralog Age Peaks — tool.io

Similar or alternative tools

Synonymous Clock Divergence
Estimate divergence time from dS assuming equal constant substitution rates on both lineages.
Reciprocal Best Hit Pairs
Validate reciprocal best-hit gene pairs from independently supplied forward and reverse maps.