📊 EMBOSS Polydot: Multi-Sequence Dot Plot Comparisons

EMBOSS Polydot is a bioinformatics tool that generates dot plots for multiple sequences simultaneously, allowing for visual comparison of a query sequence against several subject sequences. This is useful for quickly identifying regions of similarity across a small set of related sequences.

❓ What is EMBOSS Polydot?

Polydot extends the concept of a pairwise dot plot to multiple sequences. It takes one query sequence and multiple subject sequences, generating a series of dot plots (one for each query-subject pair) that can be viewed together. It helps to visually identify shared regions, repeats, or structural features across a small alignment or family.

  • Multi-Sequence Dot Plot: Compares one query against multiple subjects.

  • Visual Similarity: Creates dot plots to show matching regions.

  • Versatile Input: Works with both protein and nucleic acid sequences.

🎯 Why Use Polydot? For Visualizing Relationships in Small Datasets

EMBOSS Polydot is indispensable for:

  • 🔍 Comparative Analysis: Quickly visualizing similarities and differences between a query sequence and a few related sequences.

  • 🧬 Repeat Detection: Identifying direct or inverted repeats within a sequence (by comparing it to itself) or across multiple sequences.

  • 📊 Gene Structure Exploration: Comparing a gene sequence against its variants or homologous regions.

  • 📈 Initial Homology Assessment: Providing a rapid visual overview of relationships within a small family of sequences before detailed alignment.

  • 🎯 Educational Purposes: Demonstrating sequence similarity concepts with visual clarity.

🧑‍💻 How to Use EMBOSS Polydot on Job Dispatcher: A Step-by-Step Guide

Follow these simple steps to generate dot plots for multiple sequence comparisons with Polydot:

1️⃣ Navigate to the Tool

  1. From the main menu, go to All Tools (or search for "EMBOSS Polydot").

  2. Click the prominent Use Tool button located next to "EMBOSS Polydot."

2️⃣ Input Your Sequences

  • Locate the two input boxes (large text areas labeled "1st Input Sequence" for your query and "2nd Input Sequence" for your subject sequences) or the corresponding "upload a Sequence File" options.

  • Paste your sequences in FASTA format or upload FASTA files. Polydot supports both protein and nucleic acid sequences.

2️⃣ Input Your Sequences

  • Locate the input box (large text area) or the "upload a Sequence File" option.

  • Paste your sequences in FASTA format or upload a FASTA file.

    >ProteinA Alpha domain
MKVLWAALLVTFLAGCQAKVEQAV
>ProteinB Beta chain
GSHMLDPQFTNVYQGLRRSGFP
>ProteinC Gamma subunit
ACDEFGHIKLMNPQRSTVWY

  • Important: For each input, you can provide a sequence either by typing into the text area OR by uploading a file, but not both simultaneously. Please clear one input to proceed for both sequences.

3️⃣ Configure Parameters

  • 📝 Title: Provide a descriptive title for your job (e.g., "My Polydot Analysis").

  • 💡 Sequence Type: Select the type of sequence you are submitting:

    • Protein
    • DNA

  • 📏 WORD SIZE (wordsize): Input your own value for the minimum length of an exact match (word) to be considered.

    • Default: 6
    • Input type: Number

  • ➖ GAP (gap): Input your own value for the maximum gap allowed between matches in a diagonal.

    • Default: 10
    • Input type: Number

  • 📦 BOXIT (boxit): Choose whether to draw a box around each plot.

    • true - Default
    • false

4️⃣ Submit Your Job

  • Once your sequences are entered and parameters are set, click the Submit or Run button.

  • Your job will be dispatched to the EMBL-EBI Web Service. You will be automatically redirected to a Job Status page to monitor its progress.

5️⃣ Interpret Results

  • On the results page, you will find a series of dot plots, one for each subject sequence compared against your query.
  • Diagonal lines indicate regions of similarity. Adjusting WORD SIZE and GAP can help you find different levels of similarity.
  • ⭐ Tip: Polydot is useful for quick visual comparisons within a small group of sequences, but for large-scale comparisons or more detailed analysis, consider multiple sequence alignment tools.

💬 Need Help?

If you run into issues, please visit our Contact Us page for dedicated support. Happy visualizing!