INDIVIDUAL MCP TOOL

prime_editing_design

Design SpCas9 prime-editing pegRNAs for a substitution, insertion, deletion, or small replacement: for each usable NGG PAM it builds the spacer, a primer-binding-site (PBS) length sweep targeting a ~30 C melting temperature, the reverse-transcriptase template (RTT) that encodes the edit, and the full 3' extension, plus PE3 nicking-sgRNA suggestions 40-90 bp away on the opposite strand.

seqbench.comnone authenticationAvailability not checked

Input schema

{}

Risk classification

Potential side effects detected · medium confidence · heuristic, not a guarantee.

A tool name or description contains a write-action term.

Parent endpoint

seqbench.com

CONNECT WITH APPROVAL

Client installation

Review this server and its permissions before adding it. Secret placeholders must be set locally.

Codex

~/.codex/config.toml

[mcp_servers.seqbench-mcp]
url = "https://seqbench.com/api/mcp"
enabled = true

Claude Code

.mcp.json

{
  "mcpServers": {
    "seqbench-mcp": {
      "type": "http",
      "url": "https://seqbench.com/api/mcp"
    }
  }
}

Claude Desktop

Settings → Connectors → Add custom connector

Name: seqbench-mcp
Remote MCP URL: https://seqbench.com/api/mcp

Add this remote URL as a custom connector in Claude Desktop. Availability depends on the user plan and workspace policy.

Cursor

.cursor/mcp.json

{
  "mcpServers": {
    "seqbench-mcp": {
      "url": "https://seqbench.com/api/mcp"
    }
  }
}

Visual Studio Code

.vscode/mcp.json

Add to Visual Studio Code

{
  "servers": {
    "seqbench-mcp": {
      "type": "http",
      "url": "https://seqbench.com/api/mcp"
    }
  }
}

Generic MCP

Client-specific MCP configuration

{
  "name": "seqbench-mcp",
  "transport": "streamable-http",
  "url": "https://seqbench.com/api/mcp"
}

MCP Inspector

Run the official MCP Inspector locally and enter the indexed Streamable HTTP endpoint.

Related tools

reverse_complement — Reverse, complement and reverse complement of a DNA or RNA sequence.
gc_content — GC content, AT content and per-base composition of a sequence.
translate — Translate a nucleotide sequence to protein (single frame or all six frames; standard code).
find_orfs — Find open reading frames (ATG…stop) across all six frames.
format_sequence — Clean, case-fold, DNA↔RNA convert, reverse and line-wrap a sequence.
motif_finder — Find (overlapping) occurrences of an IUPAC motif on either strand, allowing mismatches.
reverse_translate — Back-translate a protein to DNA (most-frequent codon per organism, or degenerate IUPAC consensus).
random_sequence — Generate a random DNA, RNA or protein sequence, optionally with a target GC content.