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BioSeq

Julia's package for working on Bioinformatics with DNA, RNA and Protein Sequences

Readme

BioSeq.jl

Version 0.4.0: BioSeq

Package for working with Nucleotides and Amino Acids on The Julia Language

Installation

Pkg.init() # Only the first time you install a Julia's Package

Pkg.add("BioSeq") # Install BioSeq.jl

using BioSeq # Starting to use BioSeq

Features

  • 2-bit DNA sequence DNA2Seq for saving memory
    • Faster vectorized test for calculate percentage of GC, and test A C T G on DNA2Seq
  • 8-bit bitstype Nucleotide and AminoAcid
    • Vectors of this types can be used as DNA, RNA or Protein Sequences
    • Some string's functions working for Sequences:
      • Case conversions
      • Matching functions (search, replace and others)
    • IUPAC Regex is available for matching functions
    • PROSITE patterns are available for matching functions
    • Alignments can be represented as Matrices of this types
    • DArray of this types can be used for parallel computation
    • Memory-mapped arrays of this types can be used for huge data
  • 8-bit Bit-Level Coding Scheme for Nucleotides
  • Translation methods and genetic codes
  • Tools for using IntSet/Set/Dict as alphabets
    • Common alphabets as IntSet, including extended IUPAC
    • Dicts for generate complement for nucleotide sequences or change between 3 letter and 1 letter alphabets on Proteins
    • Test for characters on alphabet
    • Check for all characters on alphabet
    • Swap for alphabet conversions

Documentation

Demo

julia> using BioSeq

julia> const dna4alphabet = alphabet(nt"ACTG", false)
Case Insensitive Alphabet{Nucleotide} of 4 elements:

 indice   : 256-element Uint8 Array
 alphabet : 4-element Nucleotide Array

 alphabet                       indice[alphabet]
 Nucleotide (Int64)             Uint8 (Int64)

 A (65)                         0x01 (1)
 C (67)                         0x02 (2)
 T (84)                         0x03 (3)
 G (71)                         0x04 (4)


julia> dnaseq = repeat( nt"GATTACA" , 2 )
14-element Nucleotide Array:
 G
 A
 T
 T
 A
 C
 A
 G
 A
 T
 T
 A
 C
 A

julia> check(dnaseq, dna4alphabet)
true

julia> protseq = translate(dnaseq,1)
4-element AminoAcid Array:
 D
 Y
 R
 L

julia> if ismatch( prosite"<D-x-[RM]" , protseq )
         threeletters = swap(protseq, AMINO_1LETTER_TO_3 )
       end
4-element ASCIIString Array:
 "ASP"
 "TYR"
 "ARG"
 "LEU"

Contributing

Fork and send a pull request or create a GitHub issue for bug reports or feature requests

First Commit

02/17/2013

Last Touched

about 2 months ago

Commits

64 commits

Requires: