🔍 GGSEARCH2SEQ: Global-Global Sequence Similarity Search

GGSEARCH2SEQ is a bioinformatics tool from the FASTA package that performs a global-global alignment search between two sequences. It's designed to find optimal alignments across the entire length of both sequences, making it suitable for assessing overall homology between sequences that are expected to be related throughout.

❓ What is GGSEARCH2SEQ?

GGSEARCH2SEQ takes two sequences (protein or nucleic acid) and finds the best global alignment between them. It's similar to the Needleman-Wunsch algorithm but is part of the FASTA suite, providing a robust method for comprehensive pairwise comparison.

  • Global Alignment: Aligns sequences across their entire length.

  • Pairwise Comparison: Compares exactly two sequences.

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

🎯 Why Use GGSEARCH2SEQ? For Comprehensive Homology Assessment

GGSEARCH2SEQ is indispensable for:

  • 🔍 Overall Homology Detection: Confirming evolutionary relationships between two sequences that are expected to be related over their full length.

  • 🧬 Gene/Protein Ortholog Identification: Identifying orthologous genes or proteins by comparing their complete sequences.

  • 📊 Sequence Identity & Similarity: Calculating precise measures of identity and similarity for entire sequences.

  • 🎯 Large-Scale Structural Changes: Detecting significant insertions, deletions, or rearrangements across the full length of two related sequences.

  • 📈 Initial Characterization: Providing a foundational alignment for sequences whose full-length relationship is of interest.

🧑‍💻 How to Use GGSEARCH2SEQ on Job Dispatcher: A Step-by-Step Guide

Follow these simple steps to perform a global-global pairwise sequence alignment with GGSEARCH2SEQ:

1️⃣ Navigate to the Tool

  1. From the main menu, go to All Tools (or search for "GGSEARCH2SEQ").

  2. Click the prominent Use Tool button located next to "GGSEARCH2SEQ."

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. GGSEARCH2SEQ 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 GGSEARCH2SEQ Alignment").

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

    • Protein
    • DNA

  • 📊 MATRIX (matrix): Select the scoring matrix to use for your alignment.

    • BL50 (BLOSUM50) - Default
    • BL62 (BLOSUM62)
    • BP62 (BLASTP62)
    • BL80 (BLOSUM80)
    • P250 (PAM250)
    • P120 (PAM120)
    • M40, M20, M10 (MDM matrices)
    • VT160, VT120, VT80, VT40, VT20, VT10 (VTML matrices)

  • ➕ MATCH/MISMATCH SCORES (match_scores): Define scores for matches and mismatches (alternative to matrix).

    • none (N/A) - Default
    • +5/-4, +3/-2, +4/-4, +4/-8

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

    • Default: 10
    • Options: 0, -1, -2, ..., -64 (various negative values)

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

    • Default: -2
    • Options: 0, -1, -2, ..., -16 (various negative values)

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

    • 0 (MARKX 0) - Default
    • 1 (MARKX 1)
    • 2 (MARKX 2)

  • 📏 SEQUENCE RANGE (seqrange): Define the range of the sequence to be used.

    • START-END - Default

  • 📈 GRAPHICS (graphics): Choose whether to output graphical representation.

    • 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 global pairwise alignment of your two sequences.
  • The output typically shows the aligned sequences, scores, and potentially graphical representations, depending on your chosen format.
  • ⭐ Tip: GGSEARCH2SEQ is best for sequences where you expect homology across their entire length. For finding local similarities, consider tools like LALIGN or SSEARCH2SEQ.

💬 Need Help?

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