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ProtParam - Analyzing Protein Sequences

Protein sequences can be analysed by several tools, based on the ProtParam tools on the Expasy Proteomics Server. The module is part of the SeqUtils package.

Protein Sequence Format

The ProteinAnalysis class takes one argument, the protein sequence as a string and builds a sequence object using the Bio.Seq module. This is done just to make sure the sequence is a protein sequence and not anything else.

Example

>>> from Bio.SeqUtils.ProtParam import ProteinAnalysis
>>> my_seq = "MAEGEITTFTALTEKFNLPPGNYKKPKLLYCSNGGHFLRILPDGTVDGTRDRSDQHIQLQLSAESV
GEVYIKSTETGQYLAMDTSGLLYGSQTPSEECLFLERLEENHYNTYTSKKHAEKNWFVGLKKNGSCKRGPRTHYGQKAIL
FLPLPV"
>>> analysed_seq = ProteinAnalysis(my_seq)
>>> analysed_seq.molecular_weight()
17103.1617
>>> analysed_seq.gravy()
-0.597368421052632
>>> analysed_seq.count_amino_acids()
{'A': 6, 'C': 3, 'E': 12, 'D': 5, 'G': 14, 'F': 6, 'I': 5, 'H': 5, 'K': 12, 'M':
 2, 'L': 18, 'N': 7, 'Q': 6, 'P': 8, 'S': 10, 'R': 6, 'T': 13, 'W': 1, 'V': 5,
 'Y': 8}
 >>>

Available Tools

Protein Scales

protein_scale(Scale, WindowSize, Edge): The method returns a list of values which can be plotted to view the change along a protein sequence. You can set several parameters that control the computation of a scale profile, such as the window size and the window edge relative weight value. Many scales exist. Just add your favorites to the ProtParamData modules.