🌊 EMBOSS Water: Local Pairwise Sequence Alignment

EMBOSS Water is a bioinformatics tool that performs optimal local pairwise sequence alignments using the Smith-Waterman algorithm. It's designed to find the most similar regions (local alignments) between two sequences, even if the sequences are largely dissimilar overall, making it ideal for identifying conserved domains or motifs.

❓ What is EMBOSS Water?

Water aligns two sequences (protein or nucleic acid) by identifying segments within them that have the highest local similarity. Unlike global alignment tools that try to align sequences end-to-end, Water focuses on finding the best matching sub-sequences, which can be particularly useful when comparing sequences with different lengths or those that share only small regions of homology.

  • Local Alignment: Identifies the most similar segments within two sequences.

  • Smith-Waterman Algorithm: Implements a classic dynamic programming algorithm for optimal local alignment.

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

🎯 Why Use Water? For Finding Conserved Regions in Divergent Sequences

EMBOSS Water is indispensable for:

  • 🔍 Domain & Motif Discovery: Pinpointing highly conserved functional domains or short sequence motifs shared between sequences, regardless of overall similarity.

  • 🧬 Fragment Matching: Identifying where a short sequence (e.g., a primer, probe, or peptide) matches within a much longer sequence.

  • 📊 Homology Search: Discovering homologous regions even in distantly related sequences or sequences with large insertions/deletions.

  • 🎯 Gene Fusion Detection: Identifying potential gene fusion events by finding highly similar segments from different parent genes.

  • 📈 Sequence Annotation: Annotating specific regions of a sequence based on matches to known functional elements.

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

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

1️⃣ Navigate to the Tool

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

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

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. Water 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 Water 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, `mark