README

== Codon optimization based on the mRNA folding energy and the codon frequency

version 0.1


==== Requirements

EnsembleEnergy program in RNAstructure package
https://rna.urmc.rochester.edu/RNAstructure.html


==== Usage

For example,
$ mkdir output_directory
$ codon_optimization_HC.pl misc/translation_table_11 misc/codon_frequency_Rery seq/gi_21219378.fa utr/pTip.fa output_directory > result.txt
Using the translation table in "translation_table_11" and the codon frequency in "codon_frequency_Rery",
this optimizes a sequence in "gi_21219378.fa" considering the UTR sequence in "pTip.fa". 
The optimized sequences are output to "output_directory",
and the detail information is written to "result_file.txt".


==== Options

--cai_thsh
Threshold of CAI
default: 0.75

--rcc_thsh
Threshold of the rare codon count
default: 0

--adptw_thsh
Threshold of the normalized codon frequency for defining rare codons

--gen_st
Start position of the region to be optimized
default 0

--gen_sp
Stop position of the region to be optimized
default 11

NOTE:
Specify codon-wise positions using a 0-based, left-close, right-open interval. 
e.g. "--gen_st 0 --gen_sp 11" will optimize the 33 head nucleotides (11 codons) at the head of a coding sequence

--n_top
Number of the optimized sequences output to the output_directory.
default: 3

--tmp_dir
Temporary directory for EnsembleEnergy program
default: /tmp

--ithr
--nthr
Assume this run is the i-th thread in the n total threads
default: --ithr 0 --nthr 1

NOTE:
For parallelization, one can do like:
for i in `seq 0 39` ; do
codon_optimization_HC.pl --ithr $i --nthr 40 ...
done


==== History

* version 0.1
- implemented the algorithms described in [Saito et al, submitted]


==== References

Yutaka Saito, Wataru Kitagawa, Toshitaka Kumagai, Naoyuki Tajima, Yoshiyuki Nishimiya, Koichi Tamano, Yoshiaki Yasutake, Tomohiro Tamura, Tomoshi Kameda1.
Developing a codon optimization method for improved expression of recombinant proteins in actinobacteria.
submitted.


==== Contact

Yutaka Saito
yutaka.saito AT aist.go.jp