Isoform Domain Loss

Identify annotated domains lost in a supplied isoform switch.

Description

An isoform switch can change an annotated protein-domain set.

An isoform switch can change an annotated protein-domain set. Set comparison identifies original domains absent from the switched annotation.

Identify annotated domains lost in a supplied isoform switch.

When to use Isoform Domain Loss

Use this for the following task: Identify annotated domains lost in a supplied isoform switch.

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

How to use Isoform Domain Loss 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 originalDomains, switchedDomains using the field table, then run the tool.
Read lostDomains, retainedDomains, domainLoss. 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
originalDomains	Original domains	list of string; minimum entries 1; maximum entries 100000; each entry: string; minimum text length 1; maximum text length 1000000; pattern \S	Required
switchedDomains	Switched domains	list of string; minimum entries 0; maximum entries 100000; each entry: string; minimum text length 1; maximum text length 1000000; pattern \S	Required

Require distinct IDs within each domain list. Preserve original order for lost and retained domains and flag any loss.^[1]

lost = original minus switched; retained = original intersection switched

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

Output field	Meaning	Value type
lostDomains	Lost domains	list of string
retainedDomains	Retained domains	list of string
domainLoss	Domain loss	boolean

json

{
  "input": {
    "originalDomains": [
      "kinase",
      "binding"
    ],
    "switchedDomains": [
      "binding"
    ]
  },
  "output": {
    "lostDomains": [
      "kinase"
    ],
    "retainedDomains": [
      "binding"
    ],
    "domainLoss": true
  }
}

Limitations and assumptions

This does not predict domains or classify functional impact. Newly added switched domains are not returned.

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 Splice Delta Effect Rank for this operation: Rank caller-supplied splice delta effect scores without predicting clinical pathogenicity. For a complementary task, use Coding Frame Integrity for this operation: Screen an in-frame canonical DNA coding sequence using the standard ATG start and TAA/TAG/TGA stops, with chosen start/terminal-stop requirements.

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

References

Isoform Domain Loss — tool.io

Similar or alternative tools

Splice Delta Effect Rank
Rank caller-supplied splice delta effect scores without predicting clinical pathogenicity.
Coding Frame Integrity
Screen an in-frame canonical DNA coding sequence using the standard ATG start and TAA/TAG/TGA stops, with chosen start/terminal-stop requirements.