🔍 EMBOSS Stretcher: Fast Global Pairwise Alignment

EMBOSS Stretcher is a bioinformatics tool designed for fast global pairwise sequence alignment. It uses a simplified version of the Needleman-Wunsch algorithm to quickly align two sequences across their entire length, making it suitable for rapid assessment of overall similarity between closely related sequences.

❓ What is EMBOSS Stretcher?

Stretcher performs a global alignment of two sequences (protein or nucleic acid) from end-to-end. While similar to EMBOSS Needle in its global approach, Stretcher is optimized for speed, providing a quicker, though sometimes less exhaustive, alignment for highly similar sequences.

  • Global Alignment: Aligns sequences across their entire length.

  • Optimized for Speed: Provides rapid alignments for quick similarity checks.

  • Versatile Input: Supports both protein and nucleic acid sequences.

🎯 Why Use Stretcher? For Quick Global Similarity Checks

EMBOSS Stretcher is indispensable for:

  • 🔍 Rapid Homology Screening: Quickly assessing the overall similarity between two closely related sequences.

  • 🧬 Gene/Protein Variant Comparison: Comparing two versions of a gene or protein to identify large-scale differences.

  • 📊 Overall Identity Calculation: Obtaining a quick measure of percentage identity between two sequences.

  • 🎯 Initial Alignment Assessment: Performing a fast initial global alignment before diving into more detailed analysis with other tools.

  • 📈 Identifying Large-Scale Structural Changes: Detecting significant insertions, deletions, or rearrangements across the entire length of two sequences.

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

Follow these simple steps to perform a global pairwise sequence alignment with Stretcher:

1️⃣ Navigate to the Tool

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

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

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. Stretcher 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 Stretcher Alignment").

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

    • Protein
    • DNA

  • ⚙️ OUTPUT FORMAT (format): Choose the desired output format for your alignment results.

    • pair - Default
    • markx0, markx1, markx2, markx3, markx10
    • srspair, score, clustal, fasta, msf, nexus, phylip, selex

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

    • If Protein Sequence Type: (e.g., EBLOSUM62 - Default, EBLOSUM30, EPAM250, etc.)
    • If DNA Sequence Type: (e.g., EDNAFULL - Default, EDNAMAT)

  • ➖ GAP OPEN (gapopen): The penalty for opening a new gap in the alignment.

    • Default: 12
    • Options: 1, 2, ..., 25 (from STRETCHER_GAP_OPTEN_OPTIONS)

  • ➖ GAP EXTEND (gapext): The penalty for extending an existing gap.

    • Default: 2
    • Options: 1, 2, ..., 8 (from STRETCHER_GAP_EXT_OPTIONS)

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 global pairwise alignment of your two sequences.
  • The output typically shows the aligned sequences, scores, and potentially graphical representations.
  • ⭐ Tip: Stretcher is ideal for quick, initial comparisons of sequences that are expected to be very similar across their entire length. For more rigorous or divergent comparisons, consider EMBOSS Needle.

💬 Need Help?

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