Comparitive Analysis

SARS-CoV-2, SARS, and MERS

            

            from Bio import Phylo
            from io import StringIO
            

            handle = StringIO("(((SARS Tor2, SARS-CoV-2),(MERS)));")
            tree = Phylo.read(handle, "newick")
            

            Phylo.draw_ascii(tree)
            

        

            

                                              ______________________ Tor2
                        _____________________|
  _____________________|                     |______________________ SARS-CoV-2
                       |
                       |_____________________ ______________________ MERS
            

        

            

            from Bio.SeqUtils import GC
            from Bio import SeqIO
            

            gc_covid = [GC(rec.seq) for rec in SeqIO.parse('covid-19.fasta', 'fasta')]
            gc_sars = [GC(rec.seq) for rec in SeqIO.parse('SARS.fasta', 'fasta')]
            gc_mers = [GC(rec.seq) for rec in SeqIO.parse('MERS.fasta', 'fasta')]
            

        

            

            [37.97277865097148]
            [40.7616550704178]
            [41.23642883229855]
            

        

            

            from Bio import pairwise2
            from Bio.pairwise2 import format_alignment
            

            covid_seq = SeqIO.read('covid-19.fasta', 'fasta').seq
            sars_seq = SeqIO.read('SARS.fasta', 'fasta').seq
            mers_seq = SeqIO.read('MERS.fasta', 'fasta').seq
            

            covid_sars_alignments = pairwise2.align.globalxx(covid_seq[0:100], sars_seq[0:100])
            covid_mers_alignments = pairwise2.align.globalxx(covid_seq[0:100], mers_seq[0:100])
            

            format_alignment(*covid_sars_alignments[0])
            

        

            

 -ATTA-AAGGTTT-A-TAC-CTTCCCAGG-TAA-CAA--AC--CAACCAACTTTCGAT-CTCTTGT-AGAT-CT--G-TTCTCTAAACGAACTT---TAAAAT-C--TGTGTG----GCTGTCACTC--
  |||  || |  | | ||  |||    || | | |    ||  |  ||  |  ||| | ||||||  |||  ||  | || | | |||||||||   |||||  |  ||| ||    || || | ||  
 GATT-TAA-G--TGAATA-GCTT----GGCT-ATC--TCACTTC--CC--C--TCG-TTCTCTTG-CAGA-ACTTTGATT-T-T-AACGAACTTAAATAAAA-GCCCTGT-TGTTTAGC-GT-A-TCGT
            

        Score = 71
            

        

            

            format_alignment(*covid_mers_alignments[0])
            

        

            

 ATTAA--AGGTTTAT-ACCTT-CCCAGGTAACAAA-CCAACCAACTT-TCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTG-GCTGTCA-CTC---
 | | |  |||||| | ||| | ||||||  | ||| |||||||||   |||||||||||||||||||||||||||||||||||||||||||||||  ||||||  |||   
 A-T-ATTAGGTTT-TTACC-TACCCAGG--A-AAAGCCAACCAAC--CTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGT-AGCTGTC-GCTCGGC
            

        Score = 89
            

        

            

            covid_mRNA = covid_seq.transcribe()
            covid_protein = covid_mRNA.translate()
            

            sars_mRNA = sars_seq.transcribe()
            sars_protein = sars_mRNA.translate()
            

            mers_mRNA = mers_seq.transcribe()
            mers_protein = mers_mRNA.translate()
            

        

            

            from collections import Counter
            

            covid_protein_freq = Counter(covid_protein)
            sars_protein_freq = Counter(sars_protein)
            mers_protein_freq = Counter(mers_protein)
            

            from matplotlib import pyplot as plt
            from matplotlib import pylab
            

            plt.bar(covid_protein_freq.keys(), covid_protein_freq.values())
            plt.xlabel('Proteins')
            plt.ylabel('n')
            plt.title('Protein Frequency in Covid-19')
            

            plt.bar(sars_protein_freq.keys(), sars_protein_freq.values())
            plt.xlabel('Proteins')
            plt.ylabel('n')
            plt.title('Protein Frequency in SARS')
            

            plt.bar(mers_protein_freq.keys(), mers_protein_freq.values())
            plt.xlabel('Proteins')
            plt.ylabel('n')
            plt.title('Protein Frequency in MERS')
            

        

            

            from Bio.SeqUtils import molecular_weight
            

            molecular_weight(covid_seq)
            molecular_weight(sars_seq)
            molecular_weight(mers_seq)
            

        

            

            9241219.214400413
            9192097.564700488
            9299088.414500311
            

        

            

            def dot_plot(seq1, seq2, **kwargs):
                data = [
                    [
                        (seq1[i:i+1] != seq2[j:j+1])
                        for j in range(len(seq1)-1)
                    ]
                for i in range(len(seq2)-1)
                ]
                title  = kwargs.pop('title')
                xlabel = kwargs.pop('xlabel')
                ylabel = kwargs.pop('ylabel')
                pylab.imshow(data)
                pylab.title(title)
                pylab.xlabel(xlabel)
                pylab.ylabel(ylabel)
                pylab.show()
            

            short_covid_seq = covid_seq[0:100]
            short_sars_seq = sars_seq[0:100]
            short_mers_seq = mers_seq[0:100]
            

            dot_plot(
                short_covid_seq, short_sars_seq, 
                xlabel='Covid-19', 
                ylabel='SARS', 
                title='Covid-19 vs. Sars \n (first 100 bp)'
            )
            

            dot_plot(
                short_covid_seq, short_mers_seq, 
                xlabel='Covid-19', 
                ylabel='MERS', 
                title='Covid-19 vs. Mers \n (first 100 bp)'
            )
            

        

            

            import py3Dmol
            

            view1 = py3Dmol.view(query='pdb:6LU7')
            view1.setStyle({'cartoon': {'color': 'spectrum'}})
            view1.png()
            

            view2 = py3Dmol.view(query='pdb:2OG3')
            view2.setStyle({'cartoon': {'color': 'spectrum'}})
            view2.png()
            

            view3 = py3Dmol.view(query='pdb:6PXH')
            view3.setStyle({'cartoon': {'color': 'spectrum'}})
            view3.png()
            

        

SARS-CoV-2