AMIP: Average Mutual Information Profile (AMIP)

In GenomicSig: Computation of Genomic Signatures

Average Mutual Information Profile (AMIP)

Description

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.

Usage

AMIP(fasta_file, n1 = 1, n2 = 4)

Arguments

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

Details

The Average Mutual Information (AMI) provides a statistical estimate of the shared information between nucleotides situated k bases apart in the DNA sequence, where k ranges from n1 to n2. This method helps identify potential patterns or correlations in the nucleotide arrangement.

Value

This function returns a data frame containing the mutual information values for the specified nucleotide positions.

Author(s)

Dr. Anu Sharma, Dr. Shashi Bhushan Lal

References

Bauer, M., Schuster, S. M., & Sayood, K. (2008). The average mutual information profile as a genomic signature. BMC Bioinformatics, 9(1), 48.

Examples

library(GenomicSig)
AMIP(fasta_file = system.file("extdata/Nuc_sequence.fasta", package = "GenomicSig"), n1 = 1, n2 = 4)

GenomicSig documentation built on Sept. 11, 2024, 6:19 p.m.