Nuclear Localization Clusters
Scan basic Lys/Arg clusters as nuclear-localization-signal candidates.
Description
A basic-cluster screen finds uninterrupted lysine/arginine runs.
A basic-cluster screen finds uninterrupted lysine/arginine runs. Such clusters can be examined as nuclear-localization candidates in a broader biological context.1
Scan basic Lys/Arg clusters as nuclear-localization-signal candidates.
When to use Nuclear Localization Clusters
Use this tool to scan basic Lys/Arg clusters as nuclear-localization-signal candidates.
Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.
How to use Nuclear Localization Clusters and understand its results
- Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.
- Enter sequence, minimumClusterLength using the field table and calculation rules, then run the tool.
- Read clusterStarts, clusterCount. The explanation below defines the units, signs, ordering and any flags or placeholder values.
- If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.
| Input field | Meaning | Value type; see rules below | Requirement |
|---|---|---|---|
| sequence | Sequence | string | Required |
| minimumClusterLength | Minimum cluster length | number | Required |
Enter a canonical sequence and positive safe-integer minimum. Walk complete K/R runs and return one zero-based start per qualifying run with count. A minimum longer than the sequence returns no clusters.
The shared sequence helper trims outer whitespace and uppercases the sequence. It requires at least one residue from ACDEFGHIKLMNPQRSTVWY. Internal whitespace, FASTA headers, ambiguous letters and modified-residue notation are rejected. Sequence indexes refer to the normalized sequence; individual tools may preserve original strings in their returned lists as explained above.
cluster qualifies when consecutive K/R run length≥minimumClusterLength Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| clusterStarts | Cluster starts | list of number |
| clusterCount | Cluster count | number |
{
"input": {
"sequence": "AKKKKA",
"minimumClusterLength": 4
},
"output": {
"clusterStarts": [
1
],
"clusterCount": 1
}
}Limitations and assumptions
Separated and bipartite signals are not modeled. No transport, accessibility or localization evidence is examined.
Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Extremely large text inputs are rejected. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.
Alternative or Complementary methods
Use Mitochondrial Targeting Screen: Screen N-terminal mitochondrial targeting composition; not a localization verdict. For a complementary task, use Signal Peptide Core Scan: Summarize N-region charge and hydrophobic signal-peptide core.
References
-
Nuclear Localization Clusters — tool.io
Similar or alternative tools
- Mitochondrial Targeting Screen
Screen N-terminal mitochondrial targeting composition; not a localization verdict.
- Signal Peptide Core Scan
Summarize N-region charge and hydrophobic signal-peptide core.