sscu: Strength of Selected Codon Usage

The package can calculate the indexes for selective stength in codon usage in bacteria species. (1) The package can calculate the strength of selected codon usage bias (sscu, also named as s_index) based on Paul Sharp's method. The method take into account of background mutation rate, and focus only on four pairs of codons with universal translational advantages in all bacterial species. Thus the sscu index is comparable among different species. (2) Translational accuracy selection can be inferred from Akashi's test. The test tabulating all codons into four categories with the feature as conserved/variable amino acids and optimal/non-optimal codons. (3) Optimal codon lists (selected codons) can be calculated by either op_highly function (by using the highly expressed genes compared with all genes to identify optimal codons biased used in the highly expressed genes), or op_corre_CodonW/op_corre_NCprime function (by correlative method developed by Hershberg & Petrov). Users will have a list of optimal codons for further analysis, such as input to the Akashi's test. (4) The detailed codon usage information, such as RSCU value, number of optimal codons in the highly/all gene set, as well as the genomic gc3 value, can be calculate by the optimal_codon_statistics and genomic_gc3 function. (5) Furthermore, we added one test function proportion_index in the package. The function focus on the proportion of optimal codon against its corresponding non-optimal codons for the the four and six codon boxes.

Author
Yu Sun
Date of publication
None
Maintainer
Yu Sun <sunyu1357@gmail.com>
License
GPL (>= 2)
Version
2.2.0

View on Bioconductor

Man pages

akashi_test
akashi test for codon usage
genomic_gc3
genomic gc3 for an multifasta genomic file
op_corre_CodonW
Identify optimal codons by using the correlative method from...
op_corre_NCprime
Identify optimal codons by using the correlative method from...
op_highly
Identify optimal codons by using the highly expressed genes...
optimal_codon_statistics
statistical table for the optimal codons
proportion_index
optimal codons index for the four and six codon boxes
s_index
S index (Strength of Selected Codon Usage)
sscu-package
Strength of Selected Codon Usage

Files in this package

sscu/DESCRIPTION
sscu/NAMESPACE
sscu/NEWS
sscu/R
sscu/R/akashi_test.R
sscu/R/genomic_gc3.R
sscu/R/op_corre_CodonW.R
sscu/R/op_corre_NCprime.R
sscu/R/op_highly.R
sscu/R/optimal_codon_statistics.R
sscu/R/proportion_index.R
sscu/R/s_index.R
sscu/build
sscu/build/partial.rdb
sscu/inst
sscu/inst/akashi_test
sscu/inst/akashi_test/bifidos_alignments
sscu/inst/akashi_test/bifidos_alignments/0001.fas.ffn.mafft
sscu/inst/akashi_test/bifidos_alignments/0002.fas.ffn.mafft
sscu/inst/akashi_test/bifidos_alignments/0003.fas.ffn.mafft
sscu/inst/akashi_test/bifidos_alignments/0004.fas.ffn.mafft
sscu/inst/akashi_test/bifidos_alignments/0005.fas.ffn.mafft
sscu/inst/akashi_test/bifidos_alignments/0006.fas.ffn.mafft
sscu/inst/akashi_test/bifidos_alignments/0007.fas.ffn.mafft
sscu/inst/akashi_test/bifidos_alignments/0008.fas.ffn.mafft
sscu/inst/akashi_test/bifidos_alignments/0009.fas.ffn.mafft
sscu/inst/akashi_test/contingency_file_Gvag
sscu/inst/akashi_test/make_contingency_table.pl
sscu/inst/correlative_test
sscu/inst/correlative_test/Gvag.codonw
sscu/inst/correlative_test/LbDelBA1.NCprime
sscu/inst/sequences
sscu/inst/sequences/Gvag_genome_cds.ffn
sscu/inst/sequences/Gvag_highly.ffn
sscu/inst/sequences/L_kunkeei_genome_cds.ffn
sscu/inst/sequences/L_kunkeei_highly.ffn
sscu/inst/sequences/LbDelBA1_genome_cds.ffn
sscu/man
sscu/man/akashi_test.Rd
sscu/man/genomic_gc3.Rd
sscu/man/op_corre_CodonW.Rd
sscu/man/op_corre_NCprime.Rd
sscu/man/op_highly.Rd
sscu/man/optimal_codon_statistics.Rd
sscu/man/proportion_index.Rd
sscu/man/s_index.Rd
sscu/man/sscu-package.Rd
sscu/vignettes
sscu/vignettes/sscu.Rmd
sscu/vignettes/sscu.html
sscu/vignettes/sscu.pdf