BioFSharp

BioFSharp aims to be a user-friendly functional 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.

BioFSharp facilitates working with sequences in a strongly typed way and is designed to work well with F# Interactive. It provides a variety of parsers for many biological file formats and a variety of algorithms suited for bioinformatic workflows.

The core datamodel implements in ascending hierarchical order:

• Chemical elements and formulas which are a collection of elements
• Amino Acids, Nucleotides and Modifications, which all implement the common IBioItem interface
• BioCollections (BioItem,BioList,BioSeq) as representation of biological sequences

Installation

For applications and libraries

You can find all available package versions on nuget.

• dotnet CLI

  dotnet add package BioFSharp

• paket CLI

  paket add BioFSharp

• package manager

  Install-Package BioFSharp -Version 2.0.0

  Or add the package reference directly to your .*proj file:

  <PackageReference Include="BioFSharp" Version="2.0.0" />
  

For scripting and interactive notebooks

You can include the package via an inline package reference:

#r "nuget: BioFSharp"

Example

The following example shows how easy it is to start working with sequences:

Create a peptide sequence:

open BioFSharp

"PEPTIDE" |> BioArray.ofAminoAcidString

         1  PEPTIDE

Create a nucleotide sequence:

"ATGC" |> BioArray.ofNucleotideString

         1  ATGC

BioFSharp comes equipped with a broad range of features and functions to map amino acids and nucleotides.

// Returns the corresponding nucleotide of the complementary strand
Nucleotides.G |> Nucleotides.complement

// Returns the monoisotopic mass of Arginine (minus H2O)
AminoAcids.Arg |> AminoAcids.monoisoMass

156.10111102304

The various file readers in BioFSharp help to easily retrieve information and write biology-associated file formats like for example FastA:

open BioFSharp.IO

let filepathFastaA = (__SOURCE_DIRECTORY__ + "/data/Chlamy_Cp.fastA")
//reads from file to an array of FastaItems.

let fastaItems = FastA.fromFile BioArray.ofAminoAcidString filepathFastaA

This will return a sequence of FastaItems, where you can directly start working with the individual sequences represented as a BioArray of amino acids.

fastaItems |> Seq.item 0

sp|P19528| cytochrome b6/f complex subunit 4 GN=petD PE=petD.p01

         1  MSVTKKPDLS DPVLKAKLAK GMGHNTYGEP AWPNDLLYMF PVVILGTFAC VIGLSVLDPA
        61  AMGEPANPFA TPLEILPEWY FYPVFQILRV VPNKLLGVLL MAAVPAGLIT VPFIESINKF
       121  QNPYRRPIAT ILFLLGTLVA VWLGIGSTFP IDISLTLGLF *

For more detailed examples continue to explore the BioFSharp documentation. In the near future we will start to provide a cookbook like tutorial in the CSBlog.

Contributing and copyright

The project is hosted on GitHub where you can report issues, fork the project and submit pull requests. If you're adding a new public API, please also consider adding samples that can be turned into a documentation.

The library is available under the OSI-approved MIT license. For more information see the License file in the GitHub repository.