📊 EMBOSS Dotpath: Visualizing Optimal Dot Plots

EMBOSS Dotpath is a bioinformatics tool that generates an optimal dot plot for two nucleic acid or protein sequences. Unlike Dotmatcher which uses a fixed window, Dotpath uses dynamic programming to find the best path through a dot matrix, highlighting the most significant regions of similarity.

❓ What is EMBOSS Dotpath?

Dotpath takes two sequences and creates a dot plot that represents the optimal alignment path. It's particularly useful for identifying complex relationships, including rearrangements, inversions, and highly conserved segments, by tracing the best matching regions across the sequences.

  • Optimal Path Visualization: Generates dot plots that highlight the best alignment path.

  • Dynamic Programming: Uses an algorithm to find optimal matches.

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

🎯 Why Use Dotpath? For Detailed Visual Homology Detection

EMBOSS Dotpath is indispensable for:

  • 🔍 Detailed Homology Mapping: Precisely visualizing regions of similarity, including complex insertions, deletions, and inversions.

  • 🧬 Gene Rearrangement Detection: Identifying structural rearrangements within or between genes by comparing genomic sequences.

  • 📊 Repeat Analysis: Discovering direct or inverted repeats within a sequence (by comparing it to itself) or between two sequences.

  • 📈 Genome Assembly Validation: Visually confirming overlaps and contig order in genome assembly projects.

  • 🎯 Understanding Complex Relationships: Providing a clear visual aid for understanding intricate relationships between two sequences that might be difficult to discern from simple text alignments.

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

Follow these simple steps to generate an optimal dot plot for your sequences with Dotpath:

1️⃣ Navigate to the Tool

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

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

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. Dotpath 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 Dotpath 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: 4
    • Input type: Number

  • ↔️ OVERLAPS (overlaps): Choose whether to allow overlaps between reported matches.

    • yes
    • no - Default

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

    • yes - Default
    • no

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 optimal dot plot. Diagonal lines indicate regions of similarity.
  • Dotpath's output emphasizes the best-scoring paths, making complex relationships easier to discern than with simple dot plots.
  • ⭐ Tip: Dotpath is particularly useful for identifying structural rearrangements or highly conserved segments in sequences that may have undergone significant changes.

💬 Need Help?

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