Protein GRAVY
Compute grand average of Kyte–Doolittle hydropathy.
Description
GRAVY summarizes sequence hydropathy through the mean of residue scores.
GRAVY summarizes sequence hydropathy through the mean of residue scores. A single whole-sequence mean can conceal strongly different local regions.1
Compute grand average of Kyte–Doolittle hydropathy.
When to use Protein GRAVY
Use this tool to compute grand average of Kyte–Doolittle hydropathy.
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 Protein GRAVY 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 using the field table and calculation rules, then run the tool.
- Read gravy. 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 |
Enter a canonical sequence. Look up the committed Kyte–Doolittle scores and return their arithmetic mean.
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.
GRAVY=ΣKyte–Doolittle residue scores/sequenceLength Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| gravy | Gravy | number |
{
"input": {
"sequence": "AI"
},
"output": {
"gravy": 3.15
}
}Limitations and assumptions
No hydrophobic regions, membrane topology or solubility prediction is computed. Modifications and experimental conditions are not modeled.
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 Transmembrane Window Scan: Detect transmembrane helix candidates from local hydropathy windows. For a complementary task, use Peptide Hydrophobicity: Estimate a peptide retention proxy from average hydropathy and caller calibration.
References
-
Protein GRAVY — tool.io
Similar or alternative tools
- Transmembrane Window Scan
Detect transmembrane helix candidates from local hydropathy windows.
- Peptide Hydrophobicity
Estimate a peptide retention proxy from average hydropathy and caller calibration.