📊 EMBOSS Dotmatcher: Visualizing Pairwise Sequence Matches

EMBOSS Dotmatcher is a bioinformatics tool that generates dot plots for two nucleic acid or protein sequences. A dot plot is a graphical representation that helps visualize regions of similarity between two sequences, including direct matches, insertions, deletions, and inversions.

❓ What is EMBOSS Dotmatcher?

Dotmatcher takes two sequences as input and creates a 2D plot where dots are placed at coordinates where the sequences match. By adjusting parameters like window size and threshold, you can control the sensitivity of the match detection. This visual output is excellent for quickly identifying homologous regions, repeats, or structural features.

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

  • Pairwise Comparison: Compares exactly two sequences.

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

🎯 Why Use Dotmatcher? For Quick Visual Homology Detection

EMBOSS Dotmatcher is indispensable for:

  • 🔍 Identifying Homologous Regions: Quickly spotting areas of similarity between two sequences.

  • 🧬 Detecting Repeats: Visualizing direct or inverted repeats within a single sequence (by comparing it to itself) or between two sequences.

  • 📊 Gene Structure Analysis: Identifying exon-intron boundaries or gene rearrangements by comparing genomic DNA to cDNA.

  • 📈 Plasmid Mapping: Mapping features or insertions in a plasmid by comparing it to a reference.

  • 🎯 Initial Sequence Assessment: Providing a rapid visual overview of sequence relationships before performing detailed alignments.

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

Follow these simple steps to generate a dot plot for your sequences with Dotmatcher:

1️⃣ Navigate to the Tool

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

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

2️⃣ Input Your Sequences

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

  • Paste your sequences in FASTA format or upload FASTA files. Dotmatcher supports both protein and nucleic acid sequences. (For an instance, in Protein)

  • Input Sequence A (1st Input Sequence):

    >seqA
MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE
    ```

  • Input Sequence B (2nd Input Sequence):

    >seqB
MGDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAAGFSYTDANKNKGITWGEDTLMEYLENPKKYIPGTKMIFAGIKKKGERADLIAYLKKATNE
    ```

  • 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 Dot Plot Analysis").

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

    • Protein
    • DNA

  • 📊 MATRIX (matrix): Select the scoring matrix to use for your dot plot. This option dynamically changes based on your "Sequence Type" selection:

    • If Protein Sequence Type:
    • EBLOSUM62 - Default
    • EBLOSUM35, EBLOSUM40, EBLOSUM50, EBLOSUM55, EBLOSUM60, EBLOSUM65, EBLOSUM70, EBLOSUM75, EBLOSUM80, EBLOSUM85, EBLOSUM90, EBLOSUMN
    • EPAM10, EPAM20, EPAM30, EPAM40, EPAM50, EPAM60, EPAM70, EPAM80, EPAM90, EPAM100, ..., EPAM500
    • If DNA Sequence Type:
    • EDNAFULL - Default
    • EDNAMAT

  • 📏 WINDOW SIZE (windowsize): Input your own value for the size of the sliding window used for comparison. A dot is placed if the window scores above the threshold.

    • Default: 10
    • Input type: Number

  • 📉 THRESHOLD (threshold): Input your own value for the minimum score required within the window to place a dot.

    • Default: 23
    • Input type: Number

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 the generated dot plot. Diagonal lines indicate regions of similarity.
  • Direct matches appear as straight diagonal lines. Insertions/deletions appear as breaks or shifts in the diagonal. Inversions appear as diagonals in the opposite direction.
  • ⭐ Tip: Adjusting WINDOW SIZE and THRESHOLD can help you find different levels of similarity. Smaller windows and lower thresholds detect more subtle matches, while larger windows and higher thresholds find stronger, more conserved regions.

💬 Need Help?

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