propy.GetSubSeq

The prediction of functional sites (e.g. methylation) of proteins usually needs to split the total protein into a set of segments around specific amino acid. Given a specific window size p, we can obtain all segments of length equal to (2*p+1) very easily. Note that the output of the method is a list form.

Authors: Dongsheng Cao and Yizeng Liang. Date: 2012.9.2 Email: oriental-cds@163.com

propy.GetSubSeq.GetSubSequence(ProteinSequence: str, ToAA: str = 'S', window: int = 3) → List[str][source]

Get all 2*window+1 sub-sequences whose cener is ToAA in a protein.

Parameters:
  • ProteinSequence (str) – a pure problem sequence
  • ToAA (str) – the central (query point) amino acid in the sub-sequence
  • window (int) – the span
Returns:

result – contains all satisfied sub-sequences

Return type:

List[str]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetSubSequence(protein)