🔍 EMBOSS Matcher: Precise Pairwise Sequence Alignment

EMBOSS Matcher is a bioinformatics tool designed for precise pairwise sequence alignment. It identifies regions of exact or near-exact matches between two sequences, making it ideal for finding highly conserved segments or verifying sequence identity.

❓ What is EMBOSS Matcher?

Matcher performs a global alignment of two sequences, but with a focus on finding optimal local alignments or exact matches between them. Unlike tools that primarily aim for overall similarity, Matcher is excellent for pinpointing specific matching regions, especially when using a stringent scoring matrix.

  • Exact Match Focus: Identifies highly similar or identical regions between two sequences.

  • Global Alignment, Local Matches: Performs a global alignment but highlights local matches.

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

🎯 Why Use Matcher? Pinpoint Conserved Regions

EMBOSS Matcher is an indispensable tool for:

  • 🔍 Identifying Conserved Motifs: Precisely locate short, highly conserved patterns or motifs shared between two sequences.

  • 🧬 Sequence Verification: Confirming the presence of specific regions or mutations by comparing a new sequence against a known reference.

  • 📊 Primer Binding Site Analysis: Identifying exact binding sites for primers or probes in a target sequence.

  • 📈 Gene/Protein Family Comparison: Quickly finding shared, highly conserved segments between two members of a gene or protein family.

  • 🎯 Quality Control: Verifying the integrity of cloned sequences or synthetic constructs against expected designs.

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

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

1️⃣ Navigate to the Tool

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

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

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. Matcher supports both protein or 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 Matcher 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: 14
    • Options: 1, 2, 3, ..., 25 (from STRETCHER_GAP_OPTEN_OPTIONS)

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

    • Default: 4
    • Options: 1, 2, ..., 8 (from STRETCHER_GAP_EXT_OPTIONS)

  • 🔢 ALTERNATIVE MATCHES (alternatives): The maximum number of alternative matches to report.

    • Default: 1
    • Options: 0, 1, 2, 5, 10, 20

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 pairwise alignment, highlighting matching regions between your two sequences.
  • The output will typically show the aligned sequences, scores, and potentially graphical representations of the matches.
  • ⭐ Tip: Pay close attention to the score and the length of the matching regions to assess the significance of the identified similarities.

💬 Need Help?

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