🔄 EMBOSS Seqret: Sequence Retrieval & Format Conversion

EMBOSS Seqret is a versatile bioinformatics tool used for retrieving sequences from various databases or files and converting them between a wide range of sequence formats. It's an essential utility for preparing sequence data for different bioinformatics applications.

❓ What is EMBOSS Seqret?

Seqret acts as a Swiss Army knife for sequence manipulation. It can read sequences from local files or remote databases, extract specific features, reverse complement sequences, change their case, and output them in almost any common bioinformatics format. It's a fundamental tool for data preprocessing and interoperability.

  • Format Conversion: Converts sequences between numerous bioinformatics formats.

  • Sequence Retrieval: Fetches sequences from files or databases.

  • Data Preprocessing: Prepares sequences for downstream analysis by modifying their properties.

🎯 Why Use Seqret? For Flexible Sequence Handling

EMBOSS Seqret is indispensable for:

  • 🔍 Data Preparation: Preparing sequence files from one tool's output to be compatible with another tool's input requirements.

  • 🧬 Database Querying: Retrieving specific sequences from large sequence collections.

  • 📊 Batch Processing: Automating the conversion or manipulation of multiple sequence files.

  • 🎯 Quality Control: Standardizing sequence formats for consistency in workflows.

  • 📈 Customizing Output: Tailoring sequence output (e.g., case, features, range) for specific needs.

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

Follow these simple steps to retrieve or convert your sequence data with Seqret:

1️⃣ Navigate to the Tool

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

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

2️⃣ Input Your Sequence

  • Locate the input box (large text area) or the "upload a Sequence File" option.

  • Paste your sequence(s) in FASTA format or upload a FASTA file. Seqret supports a vast array of input formats, but FASTA is a common starting point.

    >ProteinA Alpha domain
MKVLWAALLVTFLAGCQAKVEQAV
>ProteinB Beta chain
GSHMLDPQFTNVYQGLRRSGFP
>ProteinC Gamma subunit
ACDEFGHIKLMNPQRSTVWY

  • Important: 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.

3️⃣ Configure Parameters

  • 📝 Title: Provide a descriptive title for your job (e.g., "My Sequence Conversion Job").

  • 💡 Sequence Type: Select the type of sequence you are submitting (Protein, DNA, or RNA).

  • ➡️ INPUT FORMAT (inputformat): Specify the format of your input sequence.

    • unknown - Default
    • gcg, embl, swiss, nbrf, pdb, fasta, fastq, genbank, clustal, phylip, ace, msf, nexus, mega, text, gff, stockholm, selex, fitch, biomart, mase, raw, experiment, abi, bam, ensembl (and many more options, see form for full list)

  • ➡️ OUTPUT FORMAT (outputformat): Choose the desired format for your output sequence.

    • fasta - Default
    • embl, swiss, nbrf, genbank, gff, text, clustal, phylip, asn1, nexus, mega, mase, fastq, sam, bam, debug (and many more options, see form for full list)

  • 🧬 FEATURE (feature): Include feature table information in the output (if available in input).

    • yes - Default
    • no

  • 1️⃣ FIRST ONLY (firstonly): Only output the first sequence from a multi-sequence input file.

    • yes
    • no - Default

  • 🔄 REVERSE (reverse): Output the reverse complement of the sequence (for nucleic acids).

    • yes
    • no - Default

  • 🔡 OUTPUT CASE (outputcase): Change the case of the output sequence characters.

    • none (No change) - Default
    • lower (lower case)
    • upper (UPPER CASE)

  • 📏 SEQUENCE RANGE (seqrange): Specify a sub-range of the sequence to output.

    • START-END - Default (Outputs the entire sequence)

4️⃣ Submit Your Job

  • Once your sequence is 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 your processed sequence in the chosen output format, reflecting any conversions or manipulations you applied.
  • Verify that the format, case, and content are as expected for your downstream applications.
  • ⭐ Tip: Seqret is invaluable for ensuring compatibility between different bioinformatics tools and pipelines. Always check the output format requirements of your next step.

💬 Need Help?

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