AMIP

The Average Mutual Information Profile (AMIP) detects long-range correlations in a given DNA sequence by estimating the shared information between nucleotides situated k bases apart.

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

AMIP function

<dl> <dt>fasta_file</dt>
<dd>Path to the input FASTA file containing the DNA sequence.</dd> <dt>n1</dt>
<dd>The starting position (in bases) for Mutual Information calculation.</dd> <dt>n2</dt>
<dd>The end position (in bases) for Mutual Information calculation.</dd></dl>

Arguments

Dr. Anu Sharma,
Dr. Shashi Bhushan Lal

Author

Average Mutual Information Profile (AMIP) — AMIP

<dl>

 <dt>fasta_file</dt>
<dd>Path to the input FASTA file containing the DNA sequence.</dd>

 <dt>n1</dt>
<dd>The starting position (in bases) for Mutual Information calculation.</dd>

 <dt>n2</dt>
<dd>The end position (in bases) for Mutual Information calculation.</dd>

</dl>

AMIP: Average Mutual Information Profile (AMIP)

Description

Usage

Value

Arguments

Author

Details

References

Examples