🔍 EMBOSS Needle: Global Pairwise Sequence Alignment

EMBOSS Needle is a bioinformatics tool that performs optimal global pairwise sequence alignments using the Needleman-Wunsch algorithm. It's designed to find the best alignment across the entire length of two sequences, including gaps, making it ideal for comparing sequences that are expected to be homologous over their full length.

❓ What is EMBOSS Needle?

Needle aligns two sequences (protein or nucleic acid) from end-to-end, attempting to maximize the number of matches and minimize the number and size of gaps across their full lengths. It's a fundamental algorithm in bioinformatics for assessing overall sequence similarity and homology.

  • Global Alignment: Aligns sequences across their entire length.

  • Needleman-Wunsch Algorithm: Implements a classic dynamic programming algorithm for optimal alignment.

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

🎯 Why Use Needle? For Comprehensive Sequence Comparison

EMBOSS Needle is indispensable for:

  • 🔍 Homology Detection: Confirming evolutionary relationships between two sequences that are expected to be homologous throughout.

  • 🧬 Gene/Protein Comparison: Comparing two entire gene or protein sequences to understand their overall similarity and shared ancestry.

  • 📊 Sequence Identity Measurement: Precisely calculating the percentage identity and similarity between two sequences over their full length.

  • 🎯 Identifying Large-Scale Rearrangements: Detecting large insertions, deletions, or inversions between two related sequences.

  • 📈 Primer/Probe Validation: Verifying the full-length binding or specificity of long primers or probes.

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

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

1️⃣ Navigate to the Tool

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

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

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. Needle 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 Needle 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: 10.0
    • Options: 100.0, 50.0, 25.0, 20.0, 15.0, 10.0, 5.0, 1.0

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

    • Default: 0.5
    • Options: 0, 0.0005, 0.001, 0.05, 0.1, 0.2, 0.4, 0.5, 0.6, 0.8, 1.0, 5.0, 10.0

  • ⚖️ End Gap Penalty (endweight): Apply a penalty for gaps at the ends of the alignment.

    • true
    • false - Default

  • ➖ END GAP OPEN (endopen): The penalty for opening a gap at the end of the alignment.

    • Default: 10
    • Options: 100, 50, 25, 20, 15, 10, 5, 1

  • ➖ END GAP EXTEND (endextend): The penalty for extending a gap at the end of the alignment.

    • Default: 0.5
    • Options: 100, 50, 25, 20, 15, 10, 5, 1

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 (including match, mismatch, and gap penalties), and potentially graphical representations.
  • ⭐ Tip: Global alignments are best for sequences that are expected to share homology across their entire length. If only parts of the sequences are similar, a local alignment tool might be more appropriate.

💬 Need Help?

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