INDIVIDUAL MCP TOOL

sirna_design

Design siRNA duplexes against an mRNA target using the established Reynolds (2004) 8-criteria score and the Ui-Tei (2004) rules, plus a siDirect-style seed-duplex Tm off-target flag (≥21.

seqbench.comnone authenticationAvailability not checked

Input schema

{}

Risk classification

Inferred read-only · medium confidence · heuristic, not a guarantee.

No write-capable action terms were found; this is not proof that invocation has no side effects.

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.