BioSequence

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`BioSequence`

[Experimental]

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BioSequence[type,"seq"]

represents the biomolecular sequence of the given type corresponding to a string "seq".

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BioSequence["seq"]

infers the type (DNA, protein, etc.) from the sequence.

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BioSequence[ent]

gives the biomolecular sequence associated with the gene or protein entity ent.

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BioSequence[type,{chem₁,chem₂,…}]

gives the biomolecular sequence with type corresponding to the given list of chemicals.

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BioSequence[type,"seq",{bond₁,bond₂,…}]

represents a biomolecular sequence with the given list of bonds.

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BioSequence["HybridStrand",{bioseq₁,bioseq₂,…},{bond₁,bond₂,…}]

represents a sequence composed of multiple motif sequences with shared primary linkage.

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BioSequence[{bioseq₁,bioseq₂,…},{bond₁,bond₂,…}]

represents a number of sequences linked only by additional bonds.

Details and Options

BioSequence[…] evaluates, if possible, to the following forms:

	BioSequence[type,"seq",bonds]	motifs (single strands of a single type)
	BioSequence["HybridStrand",{bioseq₁,bioseq₂,…},bonds]	hybrid strands (single strands of multiple types)
	BioSequence[{bioseq₁,bioseq₂,…},bonds]	sequence collections (many strands with additional bonds)

BioSequence employs the following letters to represent molecules for each type:

	"DNA"	A, C, G, T
	"CircularDNA"	A, C, G, T
	"RNA"	A, C, G, U
	"CircularRNA"	A, C, G, U
	"Peptide"	A, C, D, E, F, G, H, I, K, L, M, N, O, P, Q, R, S, T, U, V, W, Y
	"CircularPeptide"	A, C, D, E, F, G, H, I, K, L, M, N, O, P, Q, R, S, T, U, V, W, Y

The content of this table is available through the "Alphabet" property of "BioSequenceType" entities; for example through Entity["BioSequenceType","DNA"]["Alphabet"].
Here is the corresponding nucleotide for each DNA (RNA) letter:
A adenine

C cytosine

G guanine

T (U) thymine (uracil)
Similarly, here is the corresponding amino acid for each peptide letter:

	A	alanine
	C	cysteine
	D	aspartic acid
	E	glutamic acid
	F	phenylalanine
	G	glycine
	H	histidine
	I	isoleucine
	K	lysine
	L	leucine
	M	methionine
	N	asparagine
	O	pyrrolysine
	P	proline
	Q	glutamine
	R	arginine
	S	serine
	T	threonine
	U	selenocysteine
	V	valine
	W	tryptophan
	Y	tyrosine

The content of the previous tables is available through the "AlphabetRules" property of "BioSequenceType" entities, for example through Entity["BioSequenceType","DNA"]["AlphabetRules"].
The "Peptide" and "CircularPeptide" types also allow a period or asterisk (. or *) to represent where a stop in biomolecular translation occurs.
Additionally, the type can be None to represent generic sequences with no given chemical meaning.
BioSequence also allows degenerate letters that represent a number of potential chemicals.
Allowed degenerate letters for DNA and RNA include:

	B	C, G or T/U (not A)
	D	A, G or T/U (not C)
	H	A, C or T/U (not G)
	K	G or T/U (keto)
	M	A or C (amino)
	N	A, C, G or T/U (any letter)
	R	A or G (purine)
	S	C or G (strong)
	V	A, C or G (not T)
	W	A or T/U (weak)
	Y	C or T/U (pyrimidine)

Allowed degenerate letters for peptides include:
B D or N

J I or L

X A, C, D, E, F, G, H, I, K, L, M, N, O, P, Q, R, S, T, U, V, W, Y

Z E or Q
The content of the previous tables is available through the "DegenerateLetterRules" property of "BioSequenceType" entities, e.g. Entity["BioSequenceType","DNA"]["DegenerateLetterRules"].
The following letter is used as the arbitrary letter when a type and length are provided:
"DNA" or "CircularDNA" N

"RNA" or "CircularRNA" N

"Peptide" or "CircularPeptide" X
BioSequence accepts standard abbreviations in place of sequence letters.
Possible abbreviations for DNA bases include:
"dAdo" A

"dCyd" C

"dGuo" G

"dNuc" N

"dPuo" R

"dThd" T

"dPyd" Y
Possible abbreviations for RNA bases include:
"Ado" A

"Cyd" C

"Guo" G

"Nuc" N

"Puo" R

"Urd" U

"Pyd" Y
Possible abbreviations for amino acids include:

	"Ala"	A
	"Asx"	B
	"Cys"	C
	"Asp"	D
	"Glu"	E
	"Phe"	F
	"Gly"	G
	"His"	H
	"Ile"	I
	"Xle"	J
	"Lys"	K
	"Leu"	L
	"Met"	M
	"Asn"	N
	"Pyl"	O
	"Pro"	P
	"Gln"	Q
	"Arg"	R
	"Ser"	S
	"Thr"	T
	"Sec"	U
	"Val"	V
	"Trp"	W
	"Xaa"	X
	"Tyr"	Y
	"Glx"	Z

In addition to the connections implied by the sequence, BioSequence letters can be connected through additional Bond entries.
Bonds specified in the form Bond[{i,j},type] connect the chemicals corresponding to the string positions i and j through a bond of type type. For example, the hydrogen bonds connecting the "A" and the "T" in the DNA sequence "ACCT" could be represented as BioSequence["DNA","ACCT",{Bond[{1,4},"MultiHydrogen"]}].
A single bond at the sequence level can represent multiple bonds at the molecular level. In the previous example, the Bond between the "A" and the "T" represents two hydrogen bonds at the molecular level.
In a hybrid strand, bonds of the form Bond[{{i₁,i₂},{j₁,j₂}},type] connect the motif strands with indices i₁ and j₁ at positions i₂ and j₂, respectively, through a bond of the specified type. For example, the hydrogen bonds connecting the "A" and the "U" in the DNA/RNA hybrid sequence {"ACC","CCU"} could be represented as BioSequence["HybridStrand",{"ACC","CCU"},{Bond[{{1,2},{2,3}},"MultiHydrogen"]}].
In a sequence collection, bonds of the form Bond[{{i₁,i₂,i₃},{j₁,j₂, j₃}},type] connect the motif strands with indices {i₁,i₂} and {j₁,j₂} at positions i₃ and j₃, respectively, through a bond of type type.
If motif strands are being connected at the sequence collection level, either {i₁,1,i₃} or {i₁,i₃} may be used. For example, given two DNA sequences "CAC" and "CTC", the hydrogen bonds connecting the "A" of the first sequence and the "T" of the second sequence can be represented as either BioSequence[{"CAC","CTC"},Bond[{{1,1,2},{2,1,2}},"MultiHydrogen"]] or BioSequence[{"CAC","CTC"},Bond[{{1,2},{2,2}},"MultiHydrogen"]] .
For a hybrid strand in a sequence collection, all indexes are needed. For example, supposing that the DNA/RNA hybrid sequence {"ACC","CCU"} is the fourth sequence in a sequence collection, then a bond index that refers to the "U" would be {4,2,3}.
All DNA and RNA sequence letters can be connected with the "MultiHydrogen" bond type.
In peptide sequences, not all bond types apply to all sequence chemicals. The following bond types can only connect the peptide letters shown:
"DisulfideBridges" C ↔ C, U ↔ U, C ↔ U

"LactamBridges" D ↔ K, E ↔ K
For example, the type in BioSequence["Peptide","CGGGU",Bond[{1,5},type]] can be "DisulfideBridges" but not "LactamBridges".
Bonds for a motif sequence can also be entered in dot-bracket notation. This form represents the bonds of a sequence as a single string where each letter of the sequence corresponds to that position in the string. Valid characters for the bond string are either a period ("."), which represents no bond or parenthesis ("(" and ")"), or angle brackets ("<" and ">"), which represent nested bonded pairs. For example, the string "<((..>))." would be appropriate for a sequence nine letters long and would be equivalent to {Bond[{1,6}],Bond[{2,8}],Bond[{3,7}]}.
Properties "prop" of a BioSequence obtained by BioSequence[…]["prop"] include:

	"SequenceType"	the type of sequence as a "BioSequenceType" entity
	"SequenceString"	a string representing the sequence
	"SequenceBondList"	a list of all explicitly given bonds in the sequence
	"SequenceBondCount"	number of explicitly given bonds in the sequence
	"SequenceLength"	the length of the sequence
	"SequencePattern"	a string expression expanding degenerate letters
	"AbbreviationSequence"	a string representation using allowed abbreviations
	"ChemicalList"	a list of the literal chemical entities
	"ChemicalPatternList"	a list of entity patterns, allowing for degenerate letters
	"MolecularMass"	the molecular mass of the sequence
	"MolarMass"	the molar mass of the sequence
	"HELM"	HELM string of the sequence
	"Properties"	a list of the properties

Both "ChemicalList" and "ChemicalPatternList" give the particular chemicals for each term of the sequence. The former does not support degenerate letters, while the latter will represent them using Alternatives.
If the sequence has degenerate terms, its molecular mass may be an Interval.
The "HELM" property gives the Hierarchical Editing Language for Macromolecules (HELM) representation of the BioSequence.
The types available to BioSequence can also be extended by creating an EntityStore with "ExtendedBioSequenceType" entities and then registering it (EntityRegister).
The following "ExtendedBioSequenceType" properties can be defined:

	"Alphabet"	a list of the letters permitted within this sequence
	"AlphabetRules"	an association from letters to specific chemicals
	"BibliographicSource"	an external identifier documenting the sequence type
	"Caption"	the caption above the sequence in formatted output
	"ComplementLetterRules"	two-way rules defining a complement operation
	"Icon"	the icon displayed in the formatted output of the sequence
	"MolecularMassRules"	an association from letters to molecular masses

The "Icon" can be provided as either an image or the canonical name of an existing sequence type.
The "MolecularMassRules" will override the molecular masses of the chemicals given via "AlphabetRules" and allow masses to be calculated when no chemicals are given.
BioSequenceQ[bioseq] gives True only if bioseq corresponds to a valid BioSequence expression.

Examples

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Basic Examples (2)Summary of the most common use cases

Represent a DNA sequence:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-va9mni

Out[1]=1

Represent an RNA sequence:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-h92vmf

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Scope (28)Survey of the scope of standard use cases

Basic Sequences (8)

Represent a peptide sequence:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-7oas8l

Out[1]=1

Represent a circular DNA sequence:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-h1gtn2

Out[1]=1

Represent a circular RNA sequence:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-fk5qd6

Out[1]=1

Represent a circular peptide sequence:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-w29vbg

Out[1]=1

Infer the type from the sequence of letters:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-mpcu4r

Out[1]=1

In[2]:=2

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https://wolfram.com/xid/0rtag198i-4c44qd

Out[2]=2

Specify a peptide sequence using standard abbreviations:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-6455lf

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Infer the type of the sequence from standard abbreviations:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-7bj8qs

Out[1]=1

Degenerate terms can be entered as alternatives in a string expression:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-v39g94

Out[1]=1

Sequences from Entities (4)

Represent a sequence through a list of corresponding chemicals:

In[2]:=2

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https://wolfram.com/xid/0rtag198i-dpc2ea

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Degenerate letters can be specified by alternatives between chemicals:

In[3]:=3

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https://wolfram.com/xid/0rtag198i-qaw9al

Out[3]=3

Represent the DNA sequence of the BRCA1 gene:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-neevxv

Out[1]=1

Represent the peptide sequence of the protein myoglobin:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-h8e9v4

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"BioSequenceType" entities can be used as the type when constructing biomolecular sequences:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-o3ljcc

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Sequences with Bonds (4)

Bond can be used to add additional structure to the sequence:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-3aspc7

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The bond type does not need to be specified and will be inferred when needed and if possible:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-vtjg8r

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Bonds in RNA can be specified using basic dot-bracket notation:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-zqkm8w

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Represent a circular peptide with a disulfide bond:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-nbs1p

Out[1]=1

Hybrid Strands (5)

Hybrid strands are strands with multiple types of sequences bonded along their primary structure:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-ietni8

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Motif-type inference works within hybrid strands:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-bory2z

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Bonds can cross the motif sequences of a hybrid strand:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-pabyer

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Bonds at the hybrid level can refer to a connection in a given motif:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-zqj10w

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Bonds can also be specified on the motif sequences of hybrid strands:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-1dg281

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Sequence Collections (7)

Sequence collections represent a set of disconnected sequences unless additional bonds are provided:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-gm2l9r

Out[1]=1

Motif sequences can be connected by bonds at the sequence level:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-wjppw2

Out[1]=1

Sequence collections can contain any mixture of motif and hybrid strands:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-qxrssg

Out[1]=1

Type inference works on both the hybrid and motif strands in sequence collections:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-u18lkq

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Bonds can connect multiple hybrid strands:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-xewo9y

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Bonds can be specified on multiple levels in a sequence collection:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-ja8kh0

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Represent a sequence collection with peptide and circular peptide components:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-crtb97

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Generalizations & Extensions (1)Generalized and extended use cases

Extend the representation of biomolecular sequences to include Hachimoji DNA:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-1mh1kn

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Properties & Relations (28)Properties of the function, and connections to other functions

BioSequence provides a number of properties:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-o0cimk

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The types of BioSequence are entities that contain many further properties describing the sequence:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-nl102g

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Access the raw sequence string:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-v5b368

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Obtain a list of all bonds:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-bll4sz

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Count the number of bonds:

In[2]:=2

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https://wolfram.com/xid/0rtag198i-luxkvd

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Find the length of the underlying sequence:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-tml0x8

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Resolve degenerate letters into patterns over specific bases:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-u95ceu

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Obtain a raw sequence string composed of abbreviations:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-3p64rs

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Specific sequences can be resolved into lists of chemicals:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-u53lg0

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Degenerate letters can be resolved into chemical alternatives:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-dzjkx2

Out[1]=1

Access the oligonucleotide (i.e. single-strand) molecular mass varying by possible degenerate choices:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-r9nl2m

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The range of molar mass is also available for sequences with degenerate letters:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-08k1hn

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Obtain the HELM representation of a sequence:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-dt7z6a

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Define a sequence type with molecular mass rules and a custom icon:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-wo1gy2

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With defined mass rules, the molecular mass can be calculated:

In[2]:=2

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https://wolfram.com/xid/0rtag198i-bii16b

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Most properties of hybrid strands are lists of the properties of the underlying motif sequences:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-fe18wb

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In[2]:=2

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https://wolfram.com/xid/0rtag198i-7a6sd

Out[2]=2

Most properties of sequence collections are lists of lists of the underlying motif sequences:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-b6pzuu

Out[1]=1

In[2]:=2

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https://wolfram.com/xid/0rtag198i-nynzdc

Out[2]=2

In[3]:=3

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https://wolfram.com/xid/0rtag198i-tikor7

Out[3]=3

In[4]:=4

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https://wolfram.com/xid/0rtag198i-vwf2m1

Out[4]=4

The "MolecularMass" and "MolarMass" properties apply to hybrid strands as a whole:

In[1]:=1

✖

https://wolfram.com/xid/0rtag198i-9bbuzm

Out[1]=1

In[2]:=2

✖

https://wolfram.com/xid/0rtag198i-ep2faw

Out[2]=2

Mass properties also apply to sequence collections as a whole:

In[1]:=1

✖

https://wolfram.com/xid/0rtag198i-lnyp37

Out[1]=1

In[2]:=2

✖

https://wolfram.com/xid/0rtag198i-realxr

Out[2]=2

The basic letters for a given type correspond to the "Alphabet" property of "BioSequenceType" entities:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-b24djg

Out[1]=1

BioSequence motifs can be provided as input to Molecule:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-3u9fxc

Out[1]=1

A hybrid strand BioSequence can also be given as an input to Molecule:

In[1]:=1

✖

https://wolfram.com/xid/0rtag198i-ekwu85

Out[1]=1

In[2]:=2

✖

https://wolfram.com/xid/0rtag198i-vnz2j5

Out[2]=2

A BioSequence collection can also be provided to Molecule:

In[1]:=1

✖

https://wolfram.com/xid/0rtag198i-vui4lr

Out[1]=1

In[2]:=2

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https://wolfram.com/xid/0rtag198i-qsvm4a

Out[2]=2

Use ConnectedMoleculeComponents to obtain the separate molecules of a sequence collection:

In[3]:=3

✖

https://wolfram.com/xid/0rtag198i-3xt3bm

Out[3]=3

SequenceAlignment can find alignments between two instances of BioSequence:

In[1]:=1

✖

https://wolfram.com/xid/0rtag198i-04vwl0

Out[1]=1

In[2]:=2

✖

https://wolfram.com/xid/0rtag198i-fbwlp1

Out[2]=2

RandomInstance can sample fully specified instances from a degenerate BioSequence:

In[1]:=1

✖

https://wolfram.com/xid/0rtag198i-ks0ppb

Out[1]=1

BioSequenceQ can validate that a BioSequence is of a given type or has other attributes:

In[1]:=1

✖

https://wolfram.com/xid/0rtag198i-3rxn5i

Out[1]=1

BioSequenceComplement and BioSequenceReverseComplement find genetic complements of a BioSequence:

In[1]:=1

✖

https://wolfram.com/xid/0rtag198i-87hpj5

Out[1]=1

In[2]:=2

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https://wolfram.com/xid/0rtag198i-06bgqd

Out[2]=2

BioSequencePlot shows a schematic diagram of a BioSequence:

In[1]:=1

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https://wolfram.com/xid/0rtag198i-169rkz

Out[1]=1

When converting a BioSequence of type "DNA", "RNA", "CircularDNA" or "CircularRNA" to a Molecule, the sequence is interpreted to be going from the 5'  3' direction (positive-sense):

In[1]:=1

✖

https://wolfram.com/xid/0rtag198i-h5r1b1

Out[1]=1

When converting a BioSequence of type "Peptide" or "CircularPeptide" to a Molecule, the sequence is interpreted to be going from the N-terminus to the C-terminus:

In[1]:=1