Symbolic Bio Sequence Representations

Start with a small

BioSequence

representing a single codon:

In[1]:=

bioseq=BioSequence["RNA","AUG"]

Out[1]=

BioSequence

Type: RNA Sequence

Content: AUG

(3 letters)



From this bio sequence, create a

ChemicalFormula

or a

Molecule

:

In[2]:=

form=ChemicalFormula@bioseq

Out[2]=

In[3]:=

mol=Molecule@bioseq

Out[3]=

Molecule

Formula:

C

29

H

36

N

12

O

19

P

2

Atoms:

98

Bonds:

105



Check to see that the two representations are equal, using

MoleculeMatchQ

:

In[4]:=

{MoleculeMatchQ[mol,bioseq],MoleculeMatchQ[mol,form]}

Out[4]=

{True,True}

With the formula representation, find molecular mass and elemental composition:

In[5]:=

form[{"MolecularMass","ElementCounts"}]

Out[5]=



918.6

u

,

carbon

29,

hydrogen

36,

nitrogen

12,

oxygen

19,

phosphorus

2

With the molecule representation, which represents all atoms and bonds explicitly, compute topological properties and generate a 3D structure:

In[6]:=

mol[{"AromaticRingCount","HBondDonorCount"}]

Out[6]=

{5,11}

In[7]:=

MoleculePlot3D[mol,PlotTheme"Spacefilling"]

Out[7]=

Use the bio sequence representation to convert this sequence into DNA or into a peptide:

In[8]:=

BioSequenceTranscribe[bioseq]

Out[8]=

BioSequence

Type: DNA Sequence

Content: ATG

(3 letters)



In[9]:=

BioSequenceTranslate[bioseq]

Out[9]=

BioSequence

Type: Peptide Sequence

Content: M

(1 letter)



Wolfram Language Example Repository

See Also

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Symbolic Bio Sequence Representations

See Also

Related Symbols

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