GC_content

This function calculates the percentage of guanine (G) or cytosine (C) nitrogenous bases in a DNA or RNA molecule. This measure indicates the proportion of G and C bases out of an implied four total bases, which including adenine (A) and thymine (T) in DNA. And adenine and uracil (U) in RNA along with G and C.

Genomic signatures represent unique features within a species' DNA, enabling the differentiation of species and offering broad applications across various fields. This package provides essential tools for calculating these specific signatures, streamlining the process for researchers and offering a comprehensive and time-saving solution for genomic analysis.The amino acid contents are identified based on the work published by Sandberg et al. (2003) <doi:10.1016/s0378-1119(03)00581-x> and Xiao et al. (2015) <doi:10.1093/bioinformatics/btv042>. The Average Mutual Information Profiles (AMIP) values are calculated based on the work of Bauer et al. (2008) <doi:10.1186/1471-2105-9-48>. The Chaos Game Representation (CGR) plot visualization was done based on the work of Deschavanne et al. (1999) <doi:10.1093/oxfordjournals.molbev.a026048> and Jeffrey et al. (1990) <doi:10.1093/nar/18.8.2163>. The GC content is calculated based on the work published by Nakabachi et al. (2006) <doi:10.1126/science.1134196> and Barbu et al. (1956) <https://pubmed.ncbi.nlm.nih.gov/13363015>. The Oligonucleotide Frequency Derived Error Gradient (OFDEG) values are computed based on the work published by Saeed et al. (2009) <doi:10.1186/1471-2164-10-S3-S10>. The Relative Synonymous Codon Usage (RSCU) values are calculated based on the work published by Elek (2018) <https://urn.nsk.hr/urn:nbn:hr:217:686131>.

Anu Sharma 

GenomicSig

Computation of Genomic Signatures

Mailarlinga 

Shashi Bhushan Lal 

Dwijesh Chandra Mishra 

Sudhir Srivastava 

Sanjeev Kumar 

Girish Kumar Jha 

Sayanti Guha Majumdar 

Megha Garg 

Sharanbasappa 

Kabilan S

GC_content function

<dl> <dt>sequence</dt>
<dd>Input as a nucleic acid sequence of characters from fasta file.</dd></dl>

Arguments

Dr. Anu Sharma,
Dr. Girish Kumar Jha

Author

GC content of nucleic acid sequences — GC_content

<dl>

 <dt>sequence</dt>
<dd>Input as a nucleic acid sequence of characters from fasta file.</dd>

</dl>

GC_content: GC content of nucleic acid sequences

Description

Usage

Value

Arguments

Author

Details

References

Examples