FSharpBio: Documentation

FSharpBio aims to be a user-friendly library for Bioinformatics written in F#. It contains the basic data structures for common biological objects like amino acids and nucleotides based on chemical formulas and chemical elements. It facilitates some basic machine learning task as well as statistical analysis of biological data set.

Example

This example demonstrates using a function defined in FSharpBio library.

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#r "FSharpBio.dll"
open FSharpBio

Converting a peptide string to a biosequence

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let peptide1 = 
    "REYAHMIGMEYDTVQK"
    |> BioSequences.ofAminoAcidString

let peptide2 = 
    "REYAHMIGMEYDTVQK"
    |> BioSequences.ofAminoAcidString



let fAlanin = Formula.parseFormulaString "C3H5ON" 

fAlanin |> Formula.monoisoMass

fAlanin |> Formula.averageMass

Formula.add fAlanin Formula.Table.H2O  |> Formula.monoisoMass



let carboxyAmidoMethylation = ModificationInfo.createModificationWithAdd "CarboxyAmidoMethylation" ModificationInfo.ModLocation.Residual  (Formula.parseFormulaString "CH3")
 
//Carboxyamidomethylated Cysteine

AminoAcids.Cys
|> AminoAcids.setModification carboxyAmidoMethylation
|> AminoAcids.setModification carboxyAmidoMethylation
|> AminoAcids.formula

namespace FSharpBio

val peptide1 : seq<AminoAcids.AminoAcid>

Full name: Tutorial.peptide1

module BioSequences

from FSharpBio

val ofAminoAcidString : s:string -> seq<AminoAcids.AminoAcid>

Full name: FSharpBio.BioSequences.ofAminoAcidString

val peptide2 : seq<AminoAcids.AminoAcid>

Full name: Tutorial.peptide2

val fAlanin : Formula.Formula

Full name: Tutorial.fAlanin

module Formula

from FSharpBio

val parseFormulaString : strFormula:string -> Formula.Formula

Full name: FSharpBio.Formula.parseFormulaString

val monoisoMass : f:Formula.Formula -> float

Full name: FSharpBio.Formula.monoisoMass

val averageMass : f:Formula.Formula -> float

Full name: FSharpBio.Formula.averageMass

val add : f1:Formula.Formula -> f2:Formula.Formula -> Map<Elements.Element,float>

Full name: FSharpBio.Formula.add

module Table

from FSharpBio.Formula

val H2O : Formula.Formula

Full name: FSharpBio.Formula.Table.H2O

val carboxyAmidoMethylation : ModificationInfo.Modification

Full name: Tutorial.carboxyAmidoMethylation

module ModificationInfo

from FSharpBio

val createModificationWithAdd : name:string -> location:ModificationInfo.ModLocation -> formula:Formula.Formula -> ModificationInfo.Modification

Full name: FSharpBio.ModificationInfo.createModificationWithAdd

ModificationInfo.ModLocation.Residual: ModificationInfo.ModLocation = 0

module AminoAcids

from FSharpBio

union case AminoAcids.AminoAcid.Cys: AminoAcids.AminoAcid

val setModification : md:ModificationInfo.Modification -> aa:AminoAcids.AminoAcid -> AminoAcids.AminoAcid

Full name: FSharpBio.AminoAcids.setModification

val formula : aa:AminoAcids.AminoAcid -> Formula.Formula

Full name: FSharpBio.AminoAcids.formula