Homeodomain Length
Check a predicted homeodomain against caller-supplied length bounds.
Description
A homeodomain-length check compares a supplied sequence segment with caller-selected bounds.
A homeodomain-length check compares a supplied sequence segment with caller-selected bounds. Length is one feature of a domain candidate.1
Check a predicted homeodomain against caller-supplied length bounds.
When to use Homeodomain Length
Use this tool to check a predicted homeodomain against caller-supplied length bounds.
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 Homeodomain Length 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, minimumLength, maximumLength using the field table and calculation rules, then run the tool.
- Read domainLength, withinRange. 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 |
| minimumLength | Minimum length | number | Required |
| maximumLength | Maximum length | number | Required |
Enter a canonical segment and finite bounds with minimum at least one and maximum no smaller. Return segment length and inclusive flag; bounds can be fractional.
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.
withinRange=minimumLength≤sequenceLength≤maximumLength Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| domainLength | Domain length | number |
| withinRange | Within range | boolean |
{
"input": {
"sequence": "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"minimumLength": 55,
"maximumLength": 65
},
"output": {
"domainLength": 60,
"withinRange": true
}
}Limitations and assumptions
No domain boundary, conserved sequence or structural alignment is determined. Appropriate length alone does not establish a homeodomain.
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. A successfully returned false flag is an evaluated outcome; its meaning is explained above.
Alternative or Complementary methods
Use Ef Hand Loop Screen: Screen predicted EF-hand loops by length and acidic-residue count. For a complementary task, use Kinase Motif Triad: Audit the ordered VAIK, HRD, and DFG kinase-domain motifs.
References
-
Homeodomain Length — tool.io
Similar or alternative tools
- Ef Hand Loop Screen
Screen predicted EF-hand loops by length and acidic-residue count.
- Kinase Motif Triad
Audit the ordered VAIK, HRD, and DFG kinase-domain motifs.