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SeqLengthPlot v2.0.2: An All-in-One, Easy-to-Use Tool for Visualizing and Retrieving Sequence Lengths from FASTA Files

Jan 22, 2025By Dany DomĂ­nguez PĂ©rez
Dany DomĂ­nguez PĂ©rez

Are you looking for an intuitive tool to streamline your sequence analysis? 🧬 SeqLengthPlot v2.0.2 is a Python-based, all-in-one solution designed to help you visualize sequence length distributions, split sequences by customizable thresholds, and generate detailed statistics—all in one seamless workflow.

 
What Is SeqLengthPlot?
SeqLengthPlot is a versatile and easy-to-use tool for analyzing sequence lengths from FASTA files. Whether you’re working with nucleotide sequences or proteins, this tool helps you:

  • Visualize length distributions using linear and log-scale plots.
  • Retrieve sequences split by length thresholds for downstream analysis.
  • Generate detailed statistics on sequence length distributions.
     
    What’s New in SeqLengthPlot v2.0.2?
    The latest version introduces several enhancements to improve flexibility and user experience:

1. Command-Line Flexibility
With customizable command-line flags, users can now:

  • Specify input files and output directories.
  • Select sequence types (nucleotide or protein).
  • Define plotting backends for compatibility with their operating system.

2. Updated Default Behavior

  • Nucleotide sequences are handled by default unless the --prot flag is used to indicate protein sequences.
  • If optional parameters are not provided, SeqLengthPlot uses intelligent defaults to ensure smooth execution.
     

    Key Features

    Mandatory Flags:
  • -i (input file): Path to the input FASTA file (required).
    Optional Flags:
  • -o (output directory): By default, SeqLengthPlot creates a folder in the input file’s directory based on the file name, sequence type, and threshold.
  • --cutoff: Customize the sequence length cutoff (default: 200).
  • --nt: Specify nucleotide sequences (default behavior).
  • --prot: Specify protein sequences, changing file extensions to .aa.
  • --showplot: Display plots interactively in a pop-up window (otherwise, plots are saved automatically).
  • --backend: Specify the plotting backend for matplotlib:TkAgg (default for Linux/Windows), and MacOSX (for macOS).
     
    Dependencies
    SeqLengthPlot requires:
  • Python 3.x
  • Matplotlib
  • Biopython
    Ensure these dependencies are installed before running the tool.

 
Why Choose SeqLengthPlot?
SeqLengthPlot v2.0.2 offers a streamlined solution for #Bioinformatics and sequence analysis tasks. Its flexibility and ease of use make it ideal for:

  • Visualizing FASTA file content.
  • Filtering sequences by length thresholds.
  • Analyzing nucleotide and protein sequences with minimal setup.
     

    Ready to Get Started?


    Check out our detailed tutorial to learn how to install and run SeqLengthPlot, and start leveraging its powerful features today!

For more information, visit: https://doi.org/10.1093/bioadv/vbae183