BigBio = BIG DATA for Ruby

BigBio is an initiative to a create high performance libraries for big data computing in biology.

BigBio may use BioLib C/C++/D functions for increasing performance and reducing memory consumption.

This is an experimental project. If you wish to contribute subscribe to the BioRuby and/or BioLib mailing lists.


  • BigBio can translate nucleotide sequences to amino acid sequences using an EMBOSS C function, or BioRuby's translator.
  • BigBio has an ORF emitter which parses DNA/RNA sequences and emits ORFs between START_STOP or STOP_STOP codons.
  • BigBio has a FASTA file emitter, with iterates FASTA files and iterates sequences without loading everything in memory.


Iterate through a FASTA file

Read a file without loading the whole thing in memory

fasta =
fasta.each do | rec |
  print rec.descr,rec.seq

Write a FASTA file. The simple way

fasta =

Any object can be passed in, however, as long as it responds to 'descr' and 'seq.to_s', or 'id' and 'seq.to_s'. E.g.

class StorageObject
  attr_accessor :descr, :seq

mysequence =
mysequence.descr = 'Test'
mysequence.seq = "agtcta"

write the FASTA file

fasta =

Fetch ORFs from a sequence

BigBio can parse a sequence for ORFs. Together with the FastaReader little memory gets used

# get all ORFs between start and stop codons, longer than 30 bps
orfs = predictorf.startstop(30)
# get all sequences between stop codons
seqs = predictorf.stopstop(0)

Rapid DNA/RNA to amino acid translation

Translate with EMBOSS C library, if linked, otherwise use BioRuby

trn_table = Bio::Big::TranslationAdapter.translation_table(1)
translate =


The easy way

gem install bio-bigbio

in your code

require 'bigbio'


Copyright (c) 2011-2012 Pjotr Prins. See LICENSE for further details.