codon_optimization's Introduction
== 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
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