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Instant-use add-on functions for the Wolfram Language

Function Repository Resource:

 BioSequenceMoleculePlot

Source Notebook

Visualize a biomolecular sequence with highlighted residues

Contributed by: Jan Mangaldan

ResourceFunction["BioSequenceMoleculePlot"][bioseq]

creates a two-dimensional structure diagram of the biomolecular sequence bioseq, where all residues are highlighted.

Details and Options

If bioseq is a BioSequence of type "Peptide" or "CircularPeptide", individual amino acids comprising the peptide are highlighted.
If bioseq is a BioSequence of type "DNA", "RNA", "CircularDNA" or "CircularRNA", individual nucleobases are highlighted.
Hybrid strands and sequence collections are supported.
ResourceFunction["BioSequenceMoleculePlot"] returns a Graphics expression.
ResourceFunction["BioSequenceMoleculePlot"] has the same options as MoleculePlot, with the following additions:
"Highlighting"Automatichow to highlight the given BioSequence
With "Highlighting"→"ResidueSugar", the phosphate groups and sugars in DNA and RNA sequences are highlighted separately. With "Highlighting"→"ResidueBackbone", the phosphate groups and sugars are highlighted with a single color.

Examples

Basic Examples (1) 

Visualize the structure of the "beefy meaty peptide":

In[1]:=
ResourceFunction["BioSequenceMoleculePlot"][ BioSequence["Peptide", "KGDEESLA"]]
Out[1]=
Image

Scope (2) 

Visualize the structure of the circular peptide evolidine:

In[2]:=
ResourceFunction["BioSequenceMoleculePlot"][ BioSequence["CircularPeptide", "SFLPVNL"]]
Out[2]=
Image

Compare an RNA and a circular RNA sequence:

In[3]:=
{ResourceFunction["BioSequenceMoleculePlot"][ BioSequence["RNA", "AUCGCCGUG"]], ResourceFunction["BioSequenceMoleculePlot"][ BioSequence["CircularRNA", "AUCGCCGUG"]]} // GraphicsRow
Out[3]=
Image

Options (2) 

Highlighting (2) 

Highlight the sugars and phosphate groups together in a DNA-RNA hybrid strand:

In[4]:=
ResourceFunction["BioSequenceMoleculePlot"][ BioSequence[ "HybridStrand", {BioSequence["DNA", "TGC"], BioSequence["RNA", "GUA"]}], "Highlighting" -> "ResidueBackbone"]
Out[4]=
Image

Highlight the sugars and phosphate groups separately:

In[5]:=
ResourceFunction["BioSequenceMoleculePlot"][ BioSequence[ "HybridStrand", {BioSequence["DNA", "TGC"], BioSequence["RNA", "GUA"]}], "Highlighting" -> "ResidueSugar"]
Out[5]=
Image

Neat Examples (1) 

Highlight the amino acid residues in human insulin:

In[6]:=
ResourceFunction["BioSequenceMoleculePlot"][ BioSequence[{ BioSequence["Peptide", "FVNQHLCGSHLVEALYLVCGERGFFYTPKT", {}], BioSequence["Peptide", "GIVEQCCTSICSLYQLENYCN", {}]}, { Bond[{{2, 1, 6}, {2, 1, 11}}, "DisulfideBridges"], Bond[{{2, 1, 7}, {1, 1, 7}}, "DisulfideBridges"], Bond[{{2, 1, 20}, {1, 1, 19}}, "DisulfideBridges"]}]]
Out[6]=
Image

Version History

  • 1.0.0 – 07 February 2022

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License Information