WOLFRAM NOTEBOOK

DNA, RNA & Peptides

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Biomolecules such as DNA, RNA or peptides are compactly represented by a sequence of one letter abbreviations for each of the component chemicals.

Creation

In the Wolfram Language such a biomolecular sequence is a
BioSequence
object.
A DNA sequence:
BioSequence["DNA","ATAAACGTACGTTTTTAGGCT"]
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BioSequence
Type: DNA Sequence
Content: ATAAACGTACGTTTTTAGGCT 
(21 letters)
Sequence composition: A (6), C (3), G (4), T (8)
An RNA sequence:
BioSequence["RNA","AUAACGUAUGUA"]
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BioSequence
Type: RNA Sequence
Content: AUAACGUAUGUA 
(12 letters)
Sequence composition: A (5), C (1), G (2), U (4)
A circular peptide sequence:
BioSequence["CircularPeptide","ITGTSTVGVGRGVLGDQKNINTTYSTYYYLQDNTRGNGIFTYDAKYRT"]
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BioSequence
Type: Circular Peptide Sequence
Content: ITGTSTVGVGRGVLGDQKNIIFTYDAKYRT   
(48 letters)
Sequence composition: A (1), D (3), F (1), G (7), I (3),K (2), L (2), N (4), Q (2), R (3),S (2), T (9), V (3), Y (6)
BioSequences can be built from
chemical
and
gene
entities.
Build a sequence using a list of chemicals:
BioSequence"DNA",
thymine
CHEMICAL
,
cytosine
CHEMICAL
,
guanine
CHEMICAL
,
guanine
CHEMICAL
,
adenine
CHEMICAL
,
cytosine
CHEMICAL
,
thymine
CHEMICAL
,
cytosine
CHEMICAL
,
guanine
CHEMICAL
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BioSequence
Type: DNA Sequence
Content: TCGGACTCG 
(9 letters)
Sequence composition: A (1), C (3), G (3), T (2)
Build a sequence from the BRCA1 gene:
BioSequence
breast cancer 1, early onset
GENE
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BioSequence
Type: DNA Sequence
Content: GTACCTTGATTTCGTATTCTAACACTTCCA   
(81189 letters)
Species: human
Chromosome: chromosome 17
Orientation: minus
Gene: BRCA1
Positions: 41277500 down to 41196312
Sequence composition: A (22779), C (16955), G (17899), T (23556)

Properties

BioSequence
objects have many of the same properties of other chemistry objects.
The properties for the DNA sequence ATG:
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Property
Value
AbbreviationSequence
dAdodThddGuo
ChemicalList
adenine
,
thymine
,
guanine
ChemicalPatternList
adenine
,
thymine
,
guanine
HELM
RNA1{D(A)P.D(T)P.D(G)}$$$$V2.0
MetaInformation
MolarMass
884.65
g/mol
MolecularMass
884.65
u
SequenceBondCount
0
SequenceBondList
{}
SequenceLength
3
SequencePattern
ATG
SequenceString
ATG
SequenceType
DNA
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