| Type: | Package |
| Title: | Stability Analysis in Differentially Expressed Genes |
| Version: | 1.0.0 |
| Maintainer: | Babak Khorsand <khorsand@mail.um.ac.ir> |
| 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. |
| License: | GPL-2 | GPL-3 [expanded from: GPL] |
| LazyData: | true |
| Depends: | R(≥ 2.10.0) |
| RoxygenNote: | 5.0.1 |
| NeedsCompilation: | no |
| Packaged: | 2017-01-12 21:45:26 UTC; Babak |
| Author: | Babak Khorsand [aut, cre], Ehsan Sadeghnezhad [aut], Javad Zahiri [ths], Mohsen Sharifi [ths], Hassan Zare-mayvan [ths] |
| Repository: | CRAN |
| Date/Publication: | 2017-01-13 00:43:16 |
SADEG.ACGT
Description
Number and frequencies of occurrence of each nucleotide.
Usage
SADEG.ACGT(Nucleotide_Sequence)
Arguments
Nucleotide_Sequence |
Nucleotide Sequence |
Details
The Number of occurrence of each nucleotide.(A, T, C, and G). Furtheremore, The frequencies of occurrence of each nucleotide. (A
Value
Table which first row represent number of each nucleotide and row 2 represent percentage of each nucleotide.
Author(s)
Babak Khorsand
Examples
SADEG.ACGT("actagtcacgatcag")
SADEG.CAI
Description
Codon Adaption Index
Usage
SADEG.CAI(Nucleotide_Sequence)
Arguments
Nucleotide_Sequence |
Nucleotide Sequence |
Details
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.
Value
CAI
Author(s)
Babak Khorsand
Examples
SADEG.CAI(Nucleotide_Sequence="atggctgctgcagcggccagtcacgatcagaggtaagttgtcgcagcatgt")
SADEG.CodonUsage
Description
Frequency of occurrence of each Amino acids codons.
Usage
SADEG.CodonUsage(Nucleotide_Sequence)
Arguments
Nucleotide_Sequence |
Nucleotide Sequence |
Details
Frequency of occurrence of each Amino acids codons.
Value
CodonUsage
Author(s)
Babak Khorsand
Examples
SADEG.CodonUsage(Nucleotide_Sequence="atggctgcagcggccagtcacgatcagaggtaagttgtc")
SADEG.Dimer
Description
Number and frequency of each Dimers
Usage
SADEG.Dimer(Nucleotide_Sequence)
Arguments
Nucleotide_Sequence |
Nucleotide Sequence |
Details
Count the number of each Dimers and calculate frequencies of them.
Value
Table which first row represent number of each Dimers and row 2 represent percentage of each Dimers.
Author(s)
Babak Khorsand
Examples
SADEG.Dimer("actagtcacgatcag")
SADEG.DimerStackingEnergy
Description
Sum of Stacking energy of each Dimers.
Usage
SADEG.DimerStackingEnergy(Nucleotide_Sequence)
Arguments
Nucleotide_Sequence |
Nucleotide Sequence |
Details
Count the number of each Dimers and multiply by related stacking energy.
Value
Sum of Stacking energy of each Dimers.
Author(s)
Babak Khorsand
Examples
SADEG.DimerStackingEnergy("actagtcacgatcag")
SADEG.EENC
Description
Expected Effective Number Of Codon
Usage
SADEG.EENC(Nucleotide_Sequence)
Arguments
Nucleotide_Sequence |
Nucleotide Sequence |
Details
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.
Value
EENC
Author(s)
Babak Khorsand
Examples
SADEG.EENC(Nucleotide_Sequence="atggctgctgcagcggccagtcacgatcagaggtaagttgtcgcagcatgt")
SADEG.GC
Description
GC content.
Usage
SADEG.GC(Nucleotide_Sequence)
Arguments
Nucleotide_Sequence |
Nucleotide Sequence |
Details
GC content : Sum of frequencies of G and C.
Value
GC content
Author(s)
Babak Khorsand
Examples
SADEG.GC("actagtcacgatcag")
SADEG.GC1
Description
GC1 content.
Usage
SADEG.GC1(Nucleotide_Sequence)
Arguments
Nucleotide_Sequence |
Nucleotide Sequence |
Details
GC1 content : Sum of frequencies of G and C at the first position of each codon.
Value
GC1
Author(s)
Babak Khorsand
Examples
SADEG.GC1(Nucleotide_Sequence="atggctgctgcagcggccagtcacgatcagaggtaagttgtcgcagcatgt")
SADEG.GC12
Description
GC12 content.
Usage
SADEG.GC12(Nucleotide_Sequence)
Arguments
Nucleotide_Sequence |
Nucleotide Sequence |
Details
GC12 content : Sum of frequencies of G and C at first and second position of each codon.
Value
GC12
Author(s)
Babak Khorsand
Examples
SADEG.GC12(Nucleotide_Sequence="atggctgctgcagcggccagtcacgatcagaggtaagttgtcgcagcatgt")
SADEG.GC2
Description
GC2 content.
Usage
SADEG.GC2(Nucleotide_Sequence)
Arguments
Nucleotide_Sequence |
Nucleotide Sequence |
Details
GC2 content : Sum of frequencies of G and C at the second position of each codon.
Value
GC2
Author(s)
Babak Khorsand
Examples
SADEG.GC2(Nucleotide_Sequence="atggctgctgcagcggccagtcacgatcagaggtaagttgtcgcagcatgt")
SADEG.GC3
Description
GC3 content.
Usage
SADEG.GC3(Nucleotide_Sequence)
Arguments
Nucleotide_Sequence |
Nucleotide Sequence |
Details
GC3 content : Sum of frequencies of G and C at the third position of each codon.
Value
GC3
Author(s)
Babak Khorsand
Examples
SADEG.GC3(Nucleotide_Sequence="atggctgctgcagcggccagtcacgatcagaggtaagttgtcgcagcatgt")
SADEG.RSCU
Description
Relative Synonymous Codon Usage
Usage
SADEG.RSCU(Nucleotide_Sequence)
Arguments
Nucleotide_Sequence |
Nucleotide Sequence |
Details
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.
Value
RSCU
Author(s)
Babak Khorsand
Examples
SADEG.RSCU(Nucleotide_Sequence="atggctgcagcggccagtcacgatcagaggtaagttgtc")
SADEG.ReverseComplement
Description
Complement of the reversed sequence.
Usage
SADEG.ReverseComplement(Nucleotide_Sequence)
Arguments
Nucleotide_Sequence |
Nucleotide Sequence |
Details
Complement of the reversed sequence. (atcagt -> Reverse: tgacta -> Reverse-Complement: actgat)
Value
Reverse-Complement
Author(s)
Babak Khorsand
Examples
SADEG.ReverseComplement("actagtcacgatcag")
SADEG.StackingEnergy
Description
Average free energy
Usage
SADEG.StackingEnergy(Nucleotide_Sequence)
Arguments
Nucleotide_Sequence |
Nucleotide Sequence |
Details
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.
Value
StackingEnergy
Author(s)
Babak Khorsand
Examples
SADEG.StackingEnergy("actagtcacgatcag")