CRAN/E | SADEG

SADEG

Stability Analysis in Differentially Expressed Genes

Installation

About

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.

Key Metrics

Version 1.0.0
R ≥ 2.10.0
Published 2017-01-13 2708 days ago
Needs compilation? no
License GPL-2
License GPL-3
CRAN checks SADEG results

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Maintainer

Maintainer

Babak Khorsand

Authors

Babak Khorsand

aut / cre

Ehsan Sadeghnezhad

aut

Javad Zahiri

ths

Mohsen Sharifi

ths

Hassan Zare-mayvan

ths

Material

Reference manual
Package source

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Depends

R ≥ 2.10.0