BioSeq (BioFSharp)

BioSeq Module

Namespace: BioFSharp
Assembly: BioFSharp.dll

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<'TBioItem>	Sequence of objects using the IBioItem interface

Functions and values

Function or value	Description
`complement nucs` Full Usage: `complement nucs` Parameters: nucs : `Nucleotide seq` 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>`
`equal a b` Full Usage: `equal a b` Parameters: a : `BioSeq<'TBioItem>` b : `BioSeq<'TBioItem>` Returns: `bool`	Compares the elemens of two sequence a : `BioSeq<'TBioItem>` b : `BioSeq<'TBioItem>` Returns: `bool`
`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`
`mapInTriplets f input` Full Usage: `mapInTriplets f input` Parameters: f : `'a * 'a * 'a -> 'a0` input : `'a seq` - The input sequence Returns: `'a0 seq`	Builds a new collection whose elements are the result of applying the given function to each triplet of the collection. If the input sequence is not divisible into triplets, the last elements are ignored, and the result is built from the truncated sequence ending with the last valid triplet. f : `'a * 'a * 'a -> 'a0` input : `'a seq` The input sequence 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: converter : `char -> AminoAcid option` s : `'a` Returns: `BioSeq<AminoAcid>`	Generates AminoAcid sequence of one-letter-code string using given OptionConverter converter : `char -> AminoAcid option` 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: converter : `char -> Nucleotide option` s : `'a` Returns: `BioSeq<Nucleotide>`	Generates nucleotide sequence of one-letter-code string using given OptionConverter converter : `char -> Nucleotide option` s : `'a` Returns: `BioSeq<Nucleotide>`
`ofThreeLetterAminoAcidString s` Full Usage: `ofThreeLetterAminoAcidString s` Parameters: s : `'a` Returns: `BioSeq<AminoAcid>`	Generates AminoAcid sequence of one-letter-code raw string s : `'a` Returns: `BioSeq<AminoAcid>`
`reverse nucs` Full Usage: `reverse nucs` Parameters: nucs : `Nucleotide seq` 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: nucs : `Nucleotide seq` 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: input : `BioSeq<'a>` Returns: `int array`	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 array`
`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: nucs : `Nucleotide seq` Returns: `BioSeq<Nucleotide>`	Transcribe a given DNA coding strand (5'-----3') nucs : `Nucleotide seq` Returns: `BioSeq<Nucleotide>`
`transcribeTemplateStrand nucs` Full Usage: `transcribeTemplateStrand nucs` Parameters: nucs : `Nucleotide seq` 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: nucleotideOffset : `int` rnaSeq : `Nucleotide seq` Returns: `BioSeq<AminoAcid>`	translates nucleotide sequence to aminoacid sequence nucleotideOffset : `int` rnaSeq : `Nucleotide seq` Returns: `BioSeq<AminoAcid>`