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Ready-to-use examples of the Wolfram Language
GC Content in Bacteria Phyla
Analyze the proportion of guanine and cytosine bases in various bacteria genomes
Create a list of bacteria entities:
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Acetobacter pasteurianus | SPECIES SPECIFICATION |
Acidipropionibacterium acidipropionici | SPECIES SPECIFICATION |
Actinoalloteichus hymeniacidonis | SPECIES SPECIFICATION |
Actinotignum urinale | SPECIES SPECIFICATION |
Arcanobacterium phocae | SPECIES SPECIFICATION |
Bacillus anthracis | SPECIES SPECIFICATION |
Bacillus circulans | SPECIES SPECIFICATION |
Bifidobacterium pseudocatenulatum | SPECIES SPECIFICATION |
Bordetella pertussis | SPECIES SPECIFICATION |
Borreliella afzelii | SPECIES SPECIFICATION |
Clostridium carboxidivorans | SPECIES SPECIFICATION |
Corynebacterium cyclohexanicum | SPECIES SPECIFICATION |
Corynebacterium jeikeium | SPECIES SPECIFICATION |
Corynebacterium ulcerans | SPECIES SPECIFICATION |
Cutibacterium granulosum | SPECIES SPECIFICATION |
Desulfitobacterium hafniense | SPECIES SPECIFICATION |
Desulfotalea psychrophila | SPECIES SPECIFICATION |
Dickeya dadantii | SPECIES SPECIFICATION |
Francisella tularensis | SPECIES SPECIFICATION |
Helicobacter pylori | SPECIES SPECIFICATION |
Klebsiella aerogenes | SPECIES SPECIFICATION |
Klebsiella pneumoniae | SPECIES SPECIFICATION |
Lactobacillus ruminis | SPECIES SPECIFICATION |
Lactobacillus salivarius | SPECIES SPECIFICATION |
Legionella jordanis | SPECIES SPECIFICATION |
Leptospira borgpetersenii | SPECIES SPECIFICATION |
Leptospira santarosai | SPECIES SPECIFICATION |
Leptospira weilii | SPECIES SPECIFICATION |
Marichromatium purpuratum | SPECIES SPECIFICATION |
Megasphaera elsdenii | SPECIES SPECIFICATION |
Mesorhizobium australicum | SPECIES SPECIFICATION |
Microbacterium oleivorans | SPECIES SPECIFICATION |
Mycobacterium tuberculosis | SPECIES SPECIFICATION |
Potomac horse fever agent | SPECIES SPECIFICATION |
Orientia tsutsugamushi | SPECIES SPECIFICATION |
Pseudomonas aeruginosa | SPECIES SPECIFICATION |
Ralstonia solanacearum | SPECIES SPECIFICATION |
Saccharomonospora glauca | SPECIES SPECIFICATION |
Sphaerochaeta coccoides | SPECIES SPECIFICATION |
Sphingobium amiense | SPECIES SPECIFICATION |
Spirochaeta perfilievii | SPECIES SPECIFICATION |
Staphylococcus aureus | SPECIES SPECIFICATION |
Staphylococcus saprophyticus | SPECIES SPECIFICATION |
Sulfurovum lithotrophicum | SPECIES SPECIFICATION |
Tolumonas auensis | SPECIES SPECIFICATION |
Treponema caldarium | SPECIES SPECIFICATION |
Treponema paraluiscuniculi | SPECIES SPECIFICATION |
Turneriella parva | SPECIES SPECIFICATION |
Yersinia pestis | SPECIES SPECIFICATION |
Yersinia pseudotuberculosis | SPECIES SPECIFICATION |
For the selected species, use the SpeciesGenomeSummary function from the Wolfram Function Repository to retrieve genomics summary information:
In[2]:=
bacGenome=
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Compare the relation between the percentage of GC (guanine-cytosine) content and the total genome sequence length across bacteria species:
In[3]:=
gc=bacGenome[All,{"PercentageOfGC","TotalSequenceLength"}]
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Find a fit and plot the relation:
In[4]:=
fit=Fit[Normal@Values@Values@gc,{1,x},x];
In[5]:=
Show[ListPlot[gc,PlotTheme"Business"],Plot[fit,{x,30,70}],FrameLabel{"GC content (%)","sequence length (bps)"}]
Out[5]=
Compare GC-content by phyla of bacteria:
In[6]:=
phylum=EntityValue[bac,"Phylum","EntityAssociation"];
In[7]:=
BoxWhiskerChartValues@GroupBy[Normal@Normal@bacGenome[All,"PercentageOfGC"]/.Normal@phylum,FirstLast],
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