DNAmotif: Generation of motifs from DNA sequences

In DNAmotif: DNA Sequence Motifs

Generation of motifs from DNA sequences

Description

Using a fasta file as input, the motifs and its corresponding frequencies are generated, considering threshold values (window size and similarity), by making consensus segments via local alignment with gap.

Usage

DNAmotifs(fasta_file, ws, cut_off)

Arguments

fasta_file	Sequence file path (.fasta format)
ws	Window size
cut_off	Minimum similarity percentage between the motifs for generating a consensus motif

Value

final_results A dataframe of motifs and their corresponding frequncies

Examples

example_fasta = system.file("exdata/sample.fasta", package = "DNAmotif")
DNAmotifs(fasta_file = example_fasta, ws = 15, cut_off = 0.75)

DNAmotif documentation built on Sept. 30, 2024, 9:30 a.m.