📊 EMBOSS Dottup: Simple Dot Plot for Exact Matches

EMBOSS Dottup is a bioinformatics tool that generates a simple dot plot for two nucleic acid or protein sequences, focusing specifically on exact matches of a defined word size. It's a quick way to visualize regions of perfect identity between two sequences.

❓ What is EMBOSS Dottup?

Dottup takes two sequences and creates a 2D plot where dots are placed only if there's an exact match of a specified "word size" between the two sequences at that point. It's a less sensitive tool than Dotmatcher or Dotpath but is excellent for quickly identifying highly conserved, identical segments.

  • Exact Match Focus: Highlights perfect identical segments.

  • Pairwise Comparison: Compares exactly two sequences.

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

🎯 Why Use Dottup? For Identifying Perfect Matches

EMBOSS Dottup is indispensable for:

  • 🔍 Verifying Identity: Confirming the exact identity of short regions between two sequences, such as primer binding sites or cloning vectors.

  • 🧬 Detecting Perfect Repeats: Quickly visualizing direct or inverted repeats within a single sequence (by comparing it to itself) or between two sequences, where the repeats are identical.

  • 📊 Quick Homology Check: Providing a rapid visual check for highly conserved, identical regions.

  • 📈 Oligonucleotide Mapping: Visualizing where specific short oligonucleotides perfectly match a longer sequence.

  • 🎯 Quality Control: Ensuring that synthesized or cloned sequences contain expected identical regions.

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

Follow these simple steps to generate a dot plot for exact matches with Dottup:

1️⃣ Navigate to the Tool

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

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

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. Dottup 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 Dottup 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: 10
    • Input type: Number

  • 📦 BOXIT (boxit): Choose whether to draw a box around the 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 the generated dot plot. Straight diagonal lines indicate regions of exact identity of the specified word size.
  • The plot will visually highlight perfect matches, making it easy to see highly conserved segments.
  • ⭐ Tip: Dottup is best for quick visual confirmation of perfect sequence matches. For more sensitive or gapped alignments, consider Dotmatcher or Dotpath.

💬 Need Help?

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