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.

Authors: Dongsheng Cao and Yizeng Liang. Date: 2012.3.27 Email: oriental-cds@163.com

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)
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)
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)
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)
propy.AAComposition.Getkmers() → List[str][source]

Get the amino acid list of 3-mers.

Returns:result – contains 8000 tri-peptides
Return type:List[str]

Examples

>>> result = Getkmers()