propy.AAComposition¶
The module is used for computing the composition of amino acids, dipetide and 3-mers (tri-peptide) for a given protein sequence.
References
[1] | Reczko, M. and Bohr, H. (1994) The DEF data base of sequence based protein fold class predictions. Nucleic Acids Res, 22, 3616-3619. |
[2] | Hua, S. and Sun, Z. (2001) Support vector machine approach for protein subcellular localization prediction. Bioinformatics, 17, 721-728. |
[3] | Grassmann, J., Reczko, M., Suhai, S. and Edler, L. (1999) Protein fold class prediction: new methods of statistical classification. Proc Int Conf Intell Syst Mol Biol, 106-112. |
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propy.AAComposition.
CalculateAAComposition
(ProteinSequence: str) → Dict[str, float][source]¶ Calculate the composition of Amino acids for a given protein sequence.
Parameters: ProteinSequence (str) – a pure protein sequence Returns: result – contains the composition of 20 amino acids. Return type: Dict[str, float] Examples
>>> from propy.GetProteinFromUniprot import GetProteinSequence >>> protein = GetProteinSequence(ProteinID="Q9NQ39") >>> result = CalculateAAComposition(protein)
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propy.AAComposition.
CalculateAADipeptideComposition
(ProteinSequence: str) → Dict[str, float][source]¶ Calculate the composition of AADs, dipeptide and 3-mers for a given protein sequence.
Parameters: ProteinSequence (str) – a pure protein sequence Returns: result – contains all composition values of AADs, dipeptide and 3-mers (8420). Return type: Dict[str, float] Examples
>>> from propy.GetProteinFromUniprot import GetProteinSequence >>> protein = GetProteinSequence(ProteinID="Q9NQ39") >>> result = CalculateAADipeptideComposition(protein)
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propy.AAComposition.
CalculateDipeptideComposition
(ProteinSequence: str) → Dict[str, float][source]¶ Calculate the composition of dipeptidefor a given protein sequence.
Parameters: ProteinSequence (a pure protein sequence) – Returns: result – contains the composition of 400 dipeptides Return type: Dict[str, float] Examples
>>> from propy.GetProteinFromUniprot import GetProteinSequence >>> protein = GetProteinSequence(ProteinID="Q9NQ39") >>> result = CalculateDipeptideComposition(protein)
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propy.AAComposition.
GetSpectrumDict
(proteinsequence: str) → Dict[str, int][source]¶ Calcualte the spectrum descriptors of 3-mers for a given protein.
Parameters: proteinsequence (a pure protein sequence) – Returns: result – contains the composition values of 8000 3-mers Return type: Dict[str, int] Examples
>>> from propy.GetProteinFromUniprot import GetProteinSequence >>> protein = GetProteinSequence(ProteinID="Q9NQ39") >>> result = GetSpectrumDict(protein)