CUBE local toolkit can calculate some popular CUB indices such as the modified codon adaptation index (mCAI) value, codon bias index (CBI), effective number of codons (ENC), frequency of optimal codons (Fop), GC content at the third position of synonymous codon (GC3s).
Email: dyyvgug@hotmail.com
Before using, please make sure that python 3.X has been installed on your computer. When using, download the repository to the local.
CUBE toolkit is mainly divided into two parts.The first part is used to calculate the CUB indices, and the second part is used to optimize the gene sequence to increase the amount of gene expression. You can test it by our test file in example_files folder.
PART1: calculate CUB indices
If the species name you plan to calculate is in the supported_species.txt, you can use the cube.py script to calculate.If the species is not in supported_species.txt, you can use the cube_comp.py script to calculate, but the codonw and rpy2 dependent library is difficult to install on Windows, you can refer to this page to install: https://github.com/MyDinnerIsReady/codonw-slim.
cube.py optional arguments:
-h, --help show this help message and exit
-cub [CUB] The list of CUB indices that you want to calculate, for example: [CAI,gc3s], the default list is CAI and ENC
-spe [SPE] The Latin name of the species, separated by an underscore, for example: Caenorhabditis_elegans
-i [I] The FASTA file of the gene sequences that wants to calculate the cube value
-o [O] The file name of output CUB value.The default file name is 'cube.txt'
cube_comp.py optional arguments:
-h, --help show this help message and exit
-spe [SPE] The Latin name of the species, separated by an underscore, for example: Caenorhabditis_elegans
-i [I] The FASTA file of gene sequences that you want to calculate the cube value
-genome [GENOME] The FASTA file of the species genome
-gff [GFF] The annotation file GFF3 format of the species
-cub [CUB] The list of CUB indices that you want to calculate, for example: [CAI,CBI,gc3s]
-o [O] The file name of output CUB value.The default file name is 'cube.txt'
Among them, the -spe parameter followed by the species that support calculation is in supported_species.txt. The -i parameter is followed by the gene sequences for which the CUB indices need to be calculated. The example sequences is in the example_files folder.-genome and -gff parameters are followed by genome sequence and GFF3 annotation file respectively.The file format can refer to the example in the example_files folder.Before using the GFF3 file, it is recommended to use the sed_gff.sh script format.The specific command is $ bash sed_gff.sh.
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Usage example:
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(1). If the species name I plan to calculate is in the supported_species.txt:
On Linux bash or Windows cmd： python cube.py -spe Caenorhabditis_elegans -i ./example_files/PART1_calculate_CUB/input_Ce.fa
If your input sequence is not in this package current folder, remember to add your sequence path (or add our package into your .bashrc file):
dyy@Workstation:~$ python cube.py -spe Zoogloea_oleivorans -i /home/disk1/sequence.fa
(2).If the species is not in supported_species.txt:
On Linux bash or Windows cmd： python cube_comp.py -i input_Zo.fa -gff Zoogloea_oleivorans.gff -genome Zoogloea_oleivorans.fna
PART2: optimize gene sequences
This opt_seq_comp.py script is used to optimize gene sequences in order to increase the expression of heterologous proteins and endogenous genes.
opt_seq_comp.py optional arguments:
-h, --help show this help message and exit
-i [I] (Required Parameters) The file name of the original sequence. The
sequence default type is DNA sequence, if that is protein sequence,
please add '-Pro' parameter
-DNA FASTA file for DNA sequences of genes that wish to increase expression
-Pro FASTA file for protein sequences of genes that wish to increase
expression
-spe [SPE] Latin name of host species, separated by an underscore, for example:
Caenorhabditis_elegans
-genome [GENOME] The FASTA file of the species genome
-gff [GFF] The annotation file GFF3 format of the species
-o [O] The file name of output optimized sequence.The default file name is
'optimized_seq.fa'
-poly Need to remove polyN sequence
-res Need to remove restriction enzyme sites
-res_sites1 [RES_SITES1]
Restriction enzyme recognition sequence
-res_sites2 [RES_SITES2]
Restriction enzyme recognition sequence
-res_sites3 [RES_SITES3]
Restriction enzyme recognition sequence
Among them,if the -DNA and -Pro parameters are not added, the default is -DNA.That is, the input original gene sequences are DNA sequences.Here are examples of usage：
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Usage example:
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(1).If I want the host species of gene expression in supported_species.txt:
python opt_seq_comp.py -spe Komagataella_pastoris -DNA -i ./example_files/PART2_optimize_sequence/input_original_DNA.fa
(2).If the input sequence file contains protein sequences：
python opt_seq_comp.py -spe Komagataella_pastoris -Pro -i ./example_files/PART2_optimize_sequence/input_original_protein.fa
(3).If you want optimized sequences to avoid the polyN signal (polyA is known to cause premature termination of transcription and translation):
python opt_seq_comp.py -spe Komagataella_pastoris -DNA -i ./example_files/PART2_optimize_sequence/input_original_DNA.fa -poly
(4).If you want optimized sequences without corresponding restriction enzyme sites：
python opt_seq_comp.py -spe Komagataella_pastoris -DNA -i ./example_files/PART2_optimize_sequence/input_original_DNA.fa -res -res_sites1 "GAATTC"
(5).If the species is not in supported_species.txt:
python opt_seq_comp.py -i input_original_DNA.fa -gff Zoogloea_oleivorans.gff -genome Zoogloea_oleivorans.fna
Thank you and best wishes！