DNAmotifs

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.

Motifs within biological sequences show a significant role. This package utilizes a user-defined threshold value (window size and similarity) to create consensus segments or motifs through local alignment of dynamic  programming with gap and it calculates the frequency of each identified motif, offering a detailed view of their prevalence within the dataset. It allows for thorough exploration and understanding of sequence patterns and their biological importance.

Subham Ghosh

DNAmotif

DNA Sequence Motifs

UB Angadi

Md Yeasin

Dipro Sinha

Saikath Das

Mir Asif Iquebal

Sarika 

DNAmotifs function

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

Arguments

Generation of motifs from DNA sequences — DNAmotifs

<dl>

<dt>fasta_file</dt>
<dd>Sequence file path (.fasta format)</dd>

<dt>ws</dt>
<dd>Window size</dd>

<dt>cut_off</dt>
<dd>Minimum similarity percentage between the motifs for generating a consensus motif</dd>

</dl>

DNAmotifs: Generation of motifs from DNA sequences

Description

Usage

Value

Arguments

Examples