Our platform’s Sequence Editor Agent is an advanced tool designed to facilitate seamless genetic sequence editing using natural language commands. This agent supports both GenBank and FASTA formats, allowing researchers to manipulate DNA, RNA, or protein sequences with ease. By leveraging natural language processing (NLP), users can directly specify the desired edits without needing to manually alter complex sequence data, making it an intuitive tool for researchers at any level.

Key Features and Capabilities:

• Natural Language Editing:

  • The Sequence Editor allows you to make changes to any sequence using simple, natural language instructions. For example, you can input commands like "insert a restriction site after exon 3" or "delete 50 base pairs before the start codon." The agent interprets your requests and performs precise edits on the sequence, saving you time and effort compared to manual sequence manipulation.

• Flexible Editing Options:

  • Insertion and Deletion: You can insert or delete any nucleotide or amino acid sequence based on your instructions. Whether you're adding a functional motif, removing a segment of non-coding DNA, or modifying coding sequences, the agent handles it smoothly.

  • Exact Location Edits: You can specify exact nucleotide positions or amino acid residues for edits, such as "insert at position 234" or "delete from base 100 to base 150." This ensures high precision for specific sequence manipulations.

  • Relative Location Edits: If you don't know the exact location but have a feature in mind (like exons, UTRs, promoters), you can specify edits relative to these features. For example, "insert a sequence 20 base pairs downstream of the transcription start site" or "delete 30 nucleotides before the stop codon."

  • AI-Guided Editing: Unsure where to make the edits? You can let the Sequence Editor Agent suggest optimal locations for insertions, deletions, or modifications. The AI evaluates the sequence and finds the most effective or least disruptive sites for your desired changes.

• GenBank and FASTA Format Support:

  • The Sequence Editor works seamlessly with both GenBank and FASTA formats, giving researchers the flexibility to edit sequences in their preferred format. GenBank users can make edits based on annotated features like genes, CDS, or regulatory elements, while FASTA users can focus on raw sequence data.

• Feature-Based Editing in GenBank Files:

  • When working with GenBank files, the agent understands and uses annotated features such as genes, exons, introns, coding sequences (CDS), promoters, and more. This enables highly targeted edits based on biological features. For example, you can request, "insert an ATG start codon in exon 2" or "delete the promoter region upstream of gene X."

• Error-Free Sequence Updates:

  • The Sequence Editor ensures that all edits maintain the integrity of the sequence. The agent checks for frameshift errors, maintains reading frames, and ensures that essential sequence motifs remain intact after editing. This reduces the risk of unintended mutations or errors in sequence design.

• Contextual Adjustments and Suggestions:

  • The agent can provide recommendations or adjustments if an edit might disrupt essential functional regions or result in low efficiency for downstream applications like cloning, CRISPR targeting, or gene expression. It ensures that your sequence remains viable and functional after edits.

Applications and Use Cases:

• Gene Editing and Mutagenesis:

  • Researchers can easily insert or delete sequences for gene knockouts, knock-ins, or point mutations. This is particularly useful for creating variants, adding regulatory elements, or removing non-coding regions.

• Cloning and Construct Design:

  • Design cloning constructs by inserting restriction enzyme sites, adding tags (e.g., His-tags, GFP), or modifying regulatory regions. The natural language interface simplifies complex cloning designs by allowing commands like "insert EcoRI site at the 5' end of the gene."

• Synthetic Biology:

  • Design synthetic constructs or optimize existing sequences for expression by introducing codon optimizations or removing unwanted sequences, using straightforward commands like "optimize for mammalian expression" or "remove intron 4."

• Functional Genomics:

  • Modify regulatory regions, such as promoters or enhancers, for functional studies. You can easily instruct the agent to make sequence edits that would be tedious to do manually, such as "insert a TATA box 30 base pairs upstream of the transcription start site."

By offering intuitive, natural language-driven sequence editing and supporting multiple formats, the Sequence Editor Agent significantly simplifies the process of genetic manipulation. Whether working with small modifications or complex construct designs, this tool provides researchers with the flexibility and precision needed to carry out sequence alterations with ease and accuracy.