🔍 SSEARCH2SEQ: Sensitive Local Pairwise Sequence Search

SSEARCH2SEQ is a bioinformatics tool from the FASTA package that performs a sensitive local pairwise sequence search. It's designed to find optimal local alignments between two sequences, excelling at detecting subtle similarities or conserved regions even in distantly related sequences.

❓ What is SSEARCH2SEQ?

SSEARCH2SEQ implements a rigorous Smith-Waterman algorithm to find the best local alignments between two sequences (protein or nucleic acid). It is known for its high sensitivity, making it a preferred choice when you need to find all significant local matches, especially in scenarios where overall sequence similarity might be low.

  • High Sensitivity: Detects subtle local similarities.
  • Local Alignment: Focuses on the most similar segments within sequences.
  • Versatile Input: Supports both protein and nucleic acid sequences.

🎯 Why Use SSEARCH2SEQ? For Detecting Distant Homologs

SSEARCH2SEQ is indispensable for:

  • 🔍 Distant Homolog Detection: Identifying evolutionarily distant but functionally related sequences by finding conserved domains or motifs.
  • 🧬 Motif Discovery: Pinpointing short, highly conserved patterns or functional sites that might be overlooked by faster, less sensitive methods.
  • 📊 Comprehensive Local Alignment: Obtaining a thorough list of all significant local alignments between two sequences.
  • 🎯 Gene/Protein Family Characterization: Deeply analyzing shared features within a family, even across divergent members.
  • 📈 Database Searching (Pairwise): While primarily pairwise, its sensitivity makes it valuable for detailed comparison against a specific reference sequence.

🧑‍💻 How to Use SSEARCH2SEQ on Job Dispatcher: A Step-by-Step Guide

Follow these simple steps to perform a sensitive local pairwise sequence search with SSEARCH2SEQ:

1️⃣ Navigate to the Tool

  1. From the main menu, go to All Tools (or search for "SSEARCH2SEQ").
  2. Click the prominent Use Tool button located next to "SSEARCH2SEQ."

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. SSEARCH2SEQ 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 SSEARCH2SEQ Analysis").

  • 💡 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: 12 (from form code)
    • Options: 0, -1, -2, ..., -64 (various negative values from GGSEARCH2SEQ_GAP_OPTEN_OPTIONS)

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

    • Default: -2 (from form code)
    • Options: 0, -1, -2, ..., -16 (various negative values from GGSEARCH2SEQ_GAP_EXT_OPTIONS)

  • ⚙️ 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 one or more local pairwise alignments, highlighting the most significant regions of similarity between your two sequences.
  • The output will typically show the aligned segments, their scores, and potentially graphical representations, depending on your chosen format.
  • ⭐ Tip: SSEARCH2SEQ is highly sensitive and can detect more distant relationships than faster heuristic methods. Review the E-values and scores carefully to assess the statistical significance of the matches.

💬 Need Help?

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