Software for error-tolerant coding of information into DNA sequences using finite-state transducers.
For license, please see LICENSE.txt
To build:
make dnastore
make test
I have built using Apple LLVM version 7.3.0 (clang-703.0.31). You will also need Boost: http://www.boost.org/
Description of method is in doc/ directory:
cd doc
make
open trans.ps
The tests include a few examples.
To generate a code transducer with 4 nucleotides of context (this will avoid all homopolymer and dinucleotide repeats):
bin/dnastore -l 4
To encode the string "Hello World!" in DNA using this transducer:
bin/dnastore -l 4 -E "Hello World!" > HelloWorld.fasta
To decode this DNA:
bin/dnastore -l 4 -d HelloWorld.fasta
To construct a composite machine using the MIXRADAR6 block code for mixed-radix conversion:
bin/dnastore -l 4 --compose-machine data/flusher.json --compose-machine data/mixradar6.json --save-machine mixradar6-dnastore4.json
(The flusher.json file describes an outer transducer that automatically flushes MIXRADAR6 whenever the end of the file is reached.)
To encode and decode using this transducer:
bin/dnastore --load-machine mixradar6-dnastore4.json -E "Hello World!" >HelloWorld46.fasta
bin/dnastore --load-machine mixradar6-dnastore4.json -d HelloWorld46.fasta
To use Viterbi decoding instead of exact decoding:
bin/dnastore --load-machine mixradar6-dnastore4.json -V HelloWorld46.fasta --error-global
To create a 64-bit watermark synchronization code with 1 watermark bit per signal bit:
bin/dnastore -l 4 --compose-machine data/water64.1.json --save-machine watmark64-dnastore4.json
Strings encoded using this code must be a multiple of 64 bits in length:
bin/dnastore --load-machine watmark64-dnastore4.json -E "Hello World! (192 bits.)" >hw64.fa
bin/dnastore --load-machine watmark64-dnastore4.json -d hw64.fa
For a list of more options:
bin/dnastore -h
You can also look at the script doc/errdecode.pl for examples of usage (this script does a lot of benchmarking).