| Title: | Stability Analysis in Differentially Expressed Genes |
|---|---|
| Description: | We analyzed the nucleotide composition of genes with a special emphasis on stability of DNA sequences. Besides, in a variety of different organisms unequal use of synonymous codons, or codon usage bias, occurs which also show variation among genes in the same genome. Seemingly, codon usage bias is affected by both selective constraints and mutation bias which allows and enables us to examine and detect changes in these two evolutionary forces between genomes or along one genome. Therefore, we determined the codon adaptation index (CAI), effective number of codons (ENC) and codon usage analysis with calculation of the relative synonymous codon usage (RSCU), and subsequently predicted the translation efficiency and accuracy through GC-rich codon usages. Furthermore, we estimated the relative stability of the DNA sequence following calculation of the average free energy (Delta G) and Dimer base-stacking energy level. |
| Authors: | Babak Khorsand [aut, cre], Ehsan Sadeghnezhad [aut], Javad Zahiri [ths], Mohsen Sharifi [ths], Hassan Zare-mayvan [ths] |
| Maintainer: | Babak Khorsand <[email protected]> |
| License: | GPL |
| Version: | 1.0.0 |
| Built: | 2024-12-10 06:51:54 UTC |
| Source: | CRAN |
Number and frequencies of occurrence of each nucleotide.
SADEG.ACGT(Nucleotide_Sequence)SADEG.ACGT(Nucleotide_Sequence)
Nucleotide_Sequence |
Nucleotide Sequence |
The Number of occurrence of each nucleotide.(A, T, C, and G). Furtheremore, The frequencies of occurrence of each nucleotide. (A
Table which first row represent number of each nucleotide and row 2 represent percentage of each nucleotide.
Babak Khorsand
SADEG.ACGT("actagtcacgatcag")SADEG.ACGT("actagtcacgatcag")
Codon Adaption Index
SADEG.CAI(Nucleotide_Sequence)SADEG.CAI(Nucleotide_Sequence)
Nucleotide_Sequence |
Nucleotide Sequence |
Geometric mean of the RSCU values presented as relative adaptiveness value (w), The CAI for a gene is then defined as the geometric mean of w values for codons in that gene excluding methionine, tryptophan, and stop codons.
CAI
Babak Khorsand
SADEG.CAI(Nucleotide_Sequence="atggctgctgcagcggccagtcacgatcagaggtaagttgtcgcagcatgt")SADEG.CAI(Nucleotide_Sequence="atggctgctgcagcggccagtcacgatcagaggtaagttgtcgcagcatgt")
Frequency of occurrence of each Amino acids codons.
SADEG.CodonUsage(Nucleotide_Sequence)SADEG.CodonUsage(Nucleotide_Sequence)
Nucleotide_Sequence |
Nucleotide Sequence |
Frequency of occurrence of each Amino acids codons.
CodonUsage
Babak Khorsand
SADEG.CodonUsage(Nucleotide_Sequence="atggctgcagcggccagtcacgatcagaggtaagttgtc")SADEG.CodonUsage(Nucleotide_Sequence="atggctgcagcggccagtcacgatcagaggtaagttgtc")
Number and frequency of each Dimers
SADEG.Dimer(Nucleotide_Sequence)SADEG.Dimer(Nucleotide_Sequence)
Nucleotide_Sequence |
Nucleotide Sequence |
Count the number of each Dimers and calculate frequencies of them.
Table which first row represent number of each Dimers and row 2 represent percentage of each Dimers.
Babak Khorsand
SADEG.Dimer("actagtcacgatcag")SADEG.Dimer("actagtcacgatcag")
Sum of Stacking energy of each Dimers.
SADEG.DimerStackingEnergy(Nucleotide_Sequence)SADEG.DimerStackingEnergy(Nucleotide_Sequence)
Nucleotide_Sequence |
Nucleotide Sequence |
Count the number of each Dimers and multiply by related stacking energy.
Sum of Stacking energy of each Dimers.
Babak Khorsand
SADEG.DimerStackingEnergy("actagtcacgatcag")SADEG.DimerStackingEnergy("actagtcacgatcag")
Expected Effective Number Of Codon
SADEG.EENC(Nucleotide_Sequence)SADEG.EENC(Nucleotide_Sequence)
Nucleotide_Sequence |
Nucleotide Sequence |
ENC analysis was used to quantify the absolute codon usage bias by determining the degree of codon usage bias exhibited by the coding sequences, regardless of gene length and the number of amino acids. ENC values ranged between 20 and 61. ENC value of 20, indicates extreme codon usage bias using only one of the possible synonymous codons for the corresponding amino acid and value 61 denotes no bias using all possible synonymous codons equally for the corresponding amino acid. A smaller ENC value correlates with the larger extension of codon preference in a gene. It is also generally accepted that when the ENC value is less than or equal to 35, genes tend to have a significant codon bias.
EENC
Babak Khorsand
SADEG.EENC(Nucleotide_Sequence="atggctgctgcagcggccagtcacgatcagaggtaagttgtcgcagcatgt")SADEG.EENC(Nucleotide_Sequence="atggctgctgcagcggccagtcacgatcagaggtaagttgtcgcagcatgt")
GC content.
SADEG.GC(Nucleotide_Sequence)SADEG.GC(Nucleotide_Sequence)
Nucleotide_Sequence |
Nucleotide Sequence |
GC content : Sum of frequencies of G and C.
GC content
Babak Khorsand
SADEG.GC("actagtcacgatcag")SADEG.GC("actagtcacgatcag")
GC1 content.
SADEG.GC1(Nucleotide_Sequence)SADEG.GC1(Nucleotide_Sequence)
Nucleotide_Sequence |
Nucleotide Sequence |
GC1 content : Sum of frequencies of G and C at the first position of each codon.
GC1
Babak Khorsand
SADEG.GC1(Nucleotide_Sequence="atggctgctgcagcggccagtcacgatcagaggtaagttgtcgcagcatgt")SADEG.GC1(Nucleotide_Sequence="atggctgctgcagcggccagtcacgatcagaggtaagttgtcgcagcatgt")
GC12 content.
SADEG.GC12(Nucleotide_Sequence)SADEG.GC12(Nucleotide_Sequence)
Nucleotide_Sequence |
Nucleotide Sequence |
GC12 content : Sum of frequencies of G and C at first and second position of each codon.
GC12
Babak Khorsand
SADEG.GC12(Nucleotide_Sequence="atggctgctgcagcggccagtcacgatcagaggtaagttgtcgcagcatgt")SADEG.GC12(Nucleotide_Sequence="atggctgctgcagcggccagtcacgatcagaggtaagttgtcgcagcatgt")
GC2 content.
SADEG.GC2(Nucleotide_Sequence)SADEG.GC2(Nucleotide_Sequence)
Nucleotide_Sequence |
Nucleotide Sequence |
GC2 content : Sum of frequencies of G and C at the second position of each codon.
GC2
Babak Khorsand
SADEG.GC2(Nucleotide_Sequence="atggctgctgcagcggccagtcacgatcagaggtaagttgtcgcagcatgt")SADEG.GC2(Nucleotide_Sequence="atggctgctgcagcggccagtcacgatcagaggtaagttgtcgcagcatgt")
GC3 content.
SADEG.GC3(Nucleotide_Sequence)SADEG.GC3(Nucleotide_Sequence)
Nucleotide_Sequence |
Nucleotide Sequence |
GC3 content : Sum of frequencies of G and C at the third position of each codon.
GC3
Babak Khorsand
SADEG.GC3(Nucleotide_Sequence="atggctgctgcagcggccagtcacgatcagaggtaagttgtcgcagcatgt")SADEG.GC3(Nucleotide_Sequence="atggctgctgcagcggccagtcacgatcagaggtaagttgtcgcagcatgt")
Complement of the reversed sequence.
SADEG.ReverseComplement(Nucleotide_Sequence)SADEG.ReverseComplement(Nucleotide_Sequence)
Nucleotide_Sequence |
Nucleotide Sequence |
Complement of the reversed sequence. (atcagt -> Reverse: tgacta -> Reverse-Complement: actgat)
Reverse-Complement
Babak Khorsand
SADEG.ReverseComplement("actagtcacgatcag")SADEG.ReverseComplement("actagtcacgatcag")
Relative Synonymous Codon Usage
SADEG.RSCU(Nucleotide_Sequence)SADEG.RSCU(Nucleotide_Sequence)
Nucleotide_Sequence |
Nucleotide Sequence |
The Relative Synonymous Codon Usage (RSCU) is the number of times a codon appears in a gene divided by the number of expected occurrences under equal codon usage.
RSCU
Babak Khorsand
SADEG.RSCU(Nucleotide_Sequence="atggctgcagcggccagtcacgatcagaggtaagttgtc")SADEG.RSCU(Nucleotide_Sequence="atggctgcagcggccagtcacgatcagaggtaagttgtc")
Average free energy
SADEG.StackingEnergy(Nucleotide_Sequence)SADEG.StackingEnergy(Nucleotide_Sequence)
Nucleotide_Sequence |
Nucleotide Sequence |
Average free energy value was obtained via multiplying average energy of each dimer from each sequence in number of stacked bases. In order to designate and identify a product-favored process, minus sign was denoted before the average free energy (AFE) value. Lastly, all relevant stacked bases in each gene cumulatively defined the total stacking energy for respective sequences.
StackingEnergy
Babak Khorsand
SADEG.StackingEnergy("actagtcacgatcag")SADEG.StackingEnergy("actagtcacgatcag")