DNA, RNA & Peptides

Out[]=
The Wolfram|Alpha Chemistry Team
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"]
Out[]=
BioSequence
Type: DNA Sequence
Content: ATAAACGTACGTTTTTAGGCT 
(21 letters)
Sequence composition: A (6), C (3), G (4), T (8)

An RNA sequence:
BioSequence["RNA","AUAACGUAUGUA"]
Out[]=
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"]
Out[]=
BioSequence
Type: Circular Peptide Sequence
Content: ITGTSTVGVGRGVLGDQKNI…IFTYDAKYRT   
(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

Out[]=
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

Out[]=
BioSequence
Type: DNA Sequence
Content: GTACCTTGATTTCGTATTCT…AACACTTCCA   
(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:
Out[]=
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
Button["Close",NotebookClose[]]
Out[]=
Close
TOC