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BioSeq Module

This module contains the BioSeq type and its according functions. The BioSeq type is a sequence of objects using the IBioItem interface

Types

Type Description

BioSeq<'a>

Sequence of objects using the IBioItem interface

Functions and values

Function or value Description

complement nucs

Full Usage: complement nucs

Parameters:
Returns: BioSeq<Nucleotide>

Create the complement DNA or cDNA (from RNA) strand. For example, the sequence "ATGC" is converted to "TACG"

nucs : Nucleotide seq
Returns: BioSeq<Nucleotide>

initAverageMass

Full Usage: initAverageMass

Returns: 'a seq -> float

Returns a function to calculate the average mass of the given sequence !memoization

Returns: 'a seq -> float

initAverageMassWith state

Full Usage: initAverageMassWith state

Parameters:
    state : float

Returns: 'a seq -> float

Returns a function to calculate the average mass of the given sequence and initial value (e.g. H2O) !memoization

state : float
Returns: 'a seq -> float

initMonoisoMass

Full Usage: initMonoisoMass

Returns: 'a seq -> float

Returns a function to calculate the monoisotopic mass of the given sequence !memoization

Returns: 'a seq -> float

initMonoisoMassWith state

Full Usage: initMonoisoMassWith state

Parameters:
    state : float

Returns: 'a seq -> float

Returns a function to calculate the monoisotopic mass of the given sequence and initial value (e.g. H2O) !memoization

state : float
Returns: 'a seq -> float

isEqual a b

Full Usage: isEqual a b

Parameters:
    a : 'a seq
    b : 'a seq

Returns: int

Compares the elemens of two sequence

a : 'a seq
b : 'a seq
Returns: int

mapInTriplets f input

Full Usage: mapInTriplets f input

Parameters:
    f : 'a * 'a * 'a -> 'a0
    input : 'a seq

Returns: 'a0 seq

Builts a new collection whose elements are the result of applying the given function to each triplet of the collection.

f : 'a * 'a * 'a -> 'a0
input : 'a seq
Returns: 'a0 seq

ofAminoAcidString s

Full Usage: ofAminoAcidString s

Parameters:
    s : 'a

Returns: BioSeq<AminoAcid>

Generates AminoAcid sequence of one-letter-code raw string

s : 'a
Returns: BioSeq<AminoAcid>

ofAminoAcidStringWithOptionConverter converter s

Full Usage: ofAminoAcidStringWithOptionConverter converter s

Parameters:
Returns: BioSeq<AminoAcid>

Generates AminoAcid sequence of one-letter-code string using given OptionConverter

converter : AminoAcidOptionConverter
s : 'a
Returns: BioSeq<AminoAcid>

ofAminoAcidSymbolString s

Full Usage: ofAminoAcidSymbolString s

Parameters:
    s : 'a

Returns: BioSeq<AminoAcidSymbol>

Generates AminoAcidSymbol sequence of one-letter-code raw string

s : 'a
Returns: BioSeq<AminoAcidSymbol>

ofNucleotideString s

Full Usage: ofNucleotideString s

Parameters:
    s : 'a

Returns: BioSeq<Nucleotide>

Generates nucleotide sequence of one-letter-code raw string

s : 'a
Returns: BioSeq<Nucleotide>

ofNucleotideStringWithOptionConverter converter s

Full Usage: ofNucleotideStringWithOptionConverter converter s

Parameters:
Returns: BioSeq<Nucleotide>

Generates nucleotide sequence of one-letter-code string using given OptionConverter

converter : NucleotideOptionConverter
s : 'a
Returns: BioSeq<Nucleotide>

reverse nucs

Full Usage: reverse nucs

Parameters:
Returns: BioSeq<Nucleotide>

Create the reverse DNA or RNA strand. For example, the sequence "ATGC" is converted to "CGTA"

nucs : Nucleotide seq
Returns: BioSeq<Nucleotide>

reverseComplement nucs

Full Usage: reverseComplement nucs

Parameters:
Returns: BioSeq<Nucleotide>

Create the reverse complement strand meaning antiparallel DNA strand or the cDNA (from RNA) respectivly. For example, the sequence "ATGC" is converted to "GCAT". "Antiparallel" combines the two functions "Complement" and "Inverse".

nucs : Nucleotide seq
Returns: BioSeq<Nucleotide>

toAverageMass bs

Full Usage: toAverageMass bs

Parameters:
    bs : 'a seq

Returns: float

Returns average mass of the given sequence

bs : 'a seq
Returns: float

toAverageMassWith state bs

Full Usage: toAverageMassWith state bs

Parameters:
    state : float
    bs : 'a seq

Returns: float

Returns average mass of the given sequence and initial value (e.g. H2O)

state : float
bs : 'a seq
Returns: float

toCompositionVector input

Full Usage: toCompositionVector input

Parameters:
Returns: int[]

Creates an array with information about the abundacies of the distinct BioItems by converting the symbol of the BioItem to an integer and incrementing the given integer. To decrease the size of the resulting array by still having a fast performance, all indices are shifted by 65. Therefore to call the abundancy of a given BioItem, use "Resultcompositionvector.[(BioItem.symbol bioitem) - 65]"

input : BioSeq<'a>
Returns: int[]

toFormula bs

Full Usage: toFormula bs

Parameters:
    bs : 'a seq

Returns: Formula

Returns formula

bs : 'a seq
Returns: Formula

toMonoisotopicMass bs

Full Usage: toMonoisotopicMass bs

Parameters:
    bs : 'a seq

Returns: float

Returns monoisotopic mass of the given sequence

bs : 'a seq
Returns: float

toMonoisotopicMassWith state bs

Full Usage: toMonoisotopicMassWith state bs

Parameters:
    state : float
    bs : 'a seq

Returns: float

Returns monoisotopic mass of the given sequence and initial value (e.g. H2O)

state : float
bs : 'a seq
Returns: float

toString bs

Full Usage: toString bs

Parameters:
    bs : 'a seq

Returns: string

Returns string of one-letter-code

bs : 'a seq
Returns: string

transcribeCodingStrand nucs

Full Usage: transcribeCodingStrand nucs

Parameters:
Returns: BioSeq<Nucleotide>

Transcribe a given DNA coding strand (5'-----3')

nucs : Nucleotide seq
Returns: BioSeq<Nucleotide>

transcribeTemplateStrand nucs

Full Usage: transcribeTemplateStrand nucs

Parameters:
Returns: BioSeq<Nucleotide>

Transcribe a given DNA template strand (3'-----5')

nucs : Nucleotide seq
Returns: BioSeq<Nucleotide>

translate nucleotideOffset rnaSeq

Full Usage: translate nucleotideOffset rnaSeq

Parameters:
Returns: BioSeq<AminoAcid>

translates nucleotide sequence to aminoacid sequence

nucleotideOffset : int
rnaSeq : Nucleotide seq
Returns: BioSeq<AminoAcid>

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