Analyzing protein sequences with the ProtParam module.

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 = (
...     "MAEGEITTFTALTEKFNLPPGNYKKPKLLYCSNGGHFLRILPDGTVDGTRDRSDQHIQLQ"
...     "LSAESVGEVYIKSTETGQYLAMDTSGLLYGSQTPSEECLFLERLEENHYNTYTSKKHAKN"
...     "WFVGLKKNGSCKRGPRTHYGQKAILFLPLPV"
... )
>>> 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

• count_amino_acids: Simply counts the number times an amino acid is repeated in the protein sequence. Returns a dictionary {AminoAcid: Number} and also stores the dictionary in self.amino_acids_content.
• get_amino_acids_percent: The same as count_amino_acids, only returns the number in percentage of entire sequence. Returns a dictionary and stores the dictionary in self.amino_acids_content_percent.
• molecular_weight: Calculates the molecular weight of a protein.
• aromaticity: Calculates the aromaticity value of a protein according to Lobry & Gautier (1994, Nucleic Acids Res., 22, 3174-3180). It is simply the relative frequency of Phe+Trp+Tyr.
• instability_index: Implementation of the method of Guruprasad et al. (1990, Protein Engineering, 4, 155-161). This method tests a protein for stability. Any value above 40 means the protein is unstable (=has a short half life).
• flexibility: Implementation of the flexibility method of Vihinen et al. (1994, Proteins, 19, 141-149).
• isoelectric_point: This method uses the module IsoelectricPoint to calculate the pI of a protein.
• secondary_structure_fraction: This methods returns a list of the fraction of amino acids which tend to be in helix, turn or sheet.
  • Amino acids in helix: V, I, Y, F, W, L.
  • Amino acids in turn: N, P, G, S.
  • Amino acids in sheet: E, M, A, L.

  The list contains 3 values: [Helix, Turn, Sheet].

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.

• Scale: An amino acid scale is defined by a numerical value assigned to each type of amino acid. The most frequently used scales are the hydrophobicity or hydrophilicity scales and the secondary structure conformational parameters scales, but many other scales exist which are based on different chemical and physical properties of the amino acids.
• WindowSize: The window size is the length of the interval to use for the profile computation. For a window size n, we use the i - (n - 1)/2 neighboring residues on each side of residue it compute the score for residue i. The score for residue is the sum of the scale values for these amino acids, optionally weighted according to their position in the window.
• Edge : The central amino acid of the window always has a weight of 1. By default, the amino acids at the remaining window positions have the same weight, but you can make the residue at the center of the window have a larger weight than the others by setting the edge value for the residues at the beginning and end of the interval to a value between 0 and 1. For instance, for Edge=0.4 and a window size of 5 the weights will be: 0.4, 0.7, 1.0, 0.7, 0.4.