celiosantosjr/ppgbiotec_bioinformatica_i

This repository contains the scripts for the discipline of Bioinformatics applied in the postgrad course in Biotechnology

Bioinformatics 101 -- PPGBiotec

Summary:

This repository contains the scripts for the discipline of Bioinformatics applied in the postgrad course in Biotechnology.

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Author: Célio Dias Santos Jr.

Email: [email protected]

Date: 7th September 2023

Location: São Carlos, SP/Brazil

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Install to run on Windows

To run this script, you can follow the instructions for the VSCode and Python installation available in the youtube:

Instructions for installation

Script: 2nd_class_script.py

To run this script you will only need the numpy package. Alternatively you may want to plot the profiles generated by using either Excel or dedicated packages in python, such as Seaborn and Matplotlib.

To install numpy, you only need to:

$ pip install numpy seaborn matplotlib pandas

To run it locally, you will only need:

$ python3 2nd_class_script.py

And it will generate the results in the screen along with several profiles as txt files.

You alternatively can use the functions to calculate your own features of interest separately for sequences you judge important, like this:

from 2nd_class_script import solubility

sequence = 'AKAKAKAKAKAAK'

solubility(sequence, verbose=True)

I recommend you explore the functions available, defined in the script with the term def in the beginning of the line.

Summarized here, follow the functions that you can use as in the above mentioned example:

Function name	Description	Inputs
calc_aafreq	Calculates the frequencies of amino acids and test their fold-change against the average composition of water soluble proteins	calc_aafreq(seq)
mw	Calculates the molecular weight of proteins in kDa	mw(seq, verbose=True)
prot_charge	Calculates the protein charge in a given pH	prot_charge(seq, pH=7.0, verbose=True)
pI	Calculates the isoelectric point of a protein	pI(seq, verbose=True)
mol_extinc	Calculates the molecular extinction coefficient of a protein in the two states redox	mol_extinc(seq, verbose=True)
profile	Generates a profile of a protein according to the values of a selected scale [See note]	profile(seq, scale, output=f'profile_{scale_name}.tsv', window=5)
antigenicity	Calculates the segments potentially antigenic from a sequence with the Kolaskar method	antigenicity(seq, verbose=True)
hydrophobicity	Calculates the average hydrophobicity of a protein using a given scale	hydrophobicity(seq, scale='KD', verbose=True)
solubility	Estimates the solubility of a given protein by using hydrophobicity inferences	solubility(seq, verbose=True)
radius	Calculates the radius for globular and linear (gyration) proteins	radius(seq, verbose=True)
sp_vol	Calculates the specific volume of a protein in mL/g	sp_vol(seq, verbose=True)
pckg_vol	Calculates the packed volume of a protein in A^3	pckg_vol(seq, verbose=True)
instability_index	Calculates the estability of a protein using instability index (stable if < 40)	instability_index(seq, verbose=True)
aliphatic_index	Calculates the aliphatic index, which gives insights about thermostability	aliphatic_index(seq, verbose=True)
boman_index	Calculates Boman index, which gives insights about the protein-protein or membrane-protein interaction	boman_index(seq, verbose=True)
hmoment	Calculates hydrophobic moment, which gives insights about structural organization	hmoment(seq, angle=100, window=11, verbose=True)
motif_finder	Searches for a motif sequence inside a protein, returning their start/stop and match	motif_finder(motif, seq, output=False, verbose=True)

Note

You can adopt several scales for the calculations, previously available in the system, such as:

Measurement	Scale name
flexibility	bfactors
antigenicity	parker
antigenicity	kolaskar
hydrophobicity	kyte_doolitle
hydrophobicity	hopp_woods
hydrophobicity	cornette
hydrophobicity	eisenberg
hydrophobicity	rose
hydrophobicity	janin
hydrophobicity	engelman

When calculating profiles, you can modify the three variables in the lines 485-487 in the main function:

profile_graphs = True
profile_numbers = False
profile_tables = False

These lines will if the first is set to True generate graphs using seaborn in the local it is executed, if the second is set to True, it will generate tables printed on the screen, and if the 3rd is set to True you can save the results as a .tsv file.

In all cases you can get the same results for a profile using a given scale.