FASTA sequence extractor

Open FASTA sequence extractor on Happytails.ai. This view has the same page content and links, with explicit tool capabilities. Read the processing notes before using a tool.

Tool capabilities

{
  "id": "fasta-sequence-extractor",
  "category": "developer-tools",
  "built": true,
  "requirements": "Select complete FASTA records by exact identifier or extract the same one-based inclusive coordinate range from each selected record. Ranges cannot wrap or run beyond record boundaries. Alignment gaps count as positions. Output preserves the original identifier, full header and sequence case, with coordinates recorded separately in JSON and CSV. Existing annotations in a header are not recalculated after extraction. Runs locally without uploads or database lookup. Limit: 500000 combined input characters, 2000 records, 2000 validation issues, a 1000-symbol motif, 20000 matches and 10000000 symbol comparisons. Exceeding a limit rejects the complete report. Each export is limited to 3000000 characters; typed CSV allows 200000 values. Preview shows 200 rows. Processing stops after 10 seconds.",
  "implementation": {
    "fields": [
      {
        "key": "alphabet",
        "label": "Sequence alphabet",
        "value": "dna",
        "type": "select",
        "values": [
          "dna",
          "rna",
          "protein"
        ]
      },
      {
        "key": "allowGaps",
        "label": "Allow alignment gaps (-)",
        "value": "false",
        "type": "select",
        "values": [
          "false",
          "true"
        ]
      },
      {
        "key": "recordIds",
        "label": "Record identifiers",
        "value": "sample",
        "type": "textarea",
        "maxLength": 500000,
        "help": "Enter one exact first-token identifier per line. Duplicate requests and missing identifiers are rejected. Requested order determines output order."
      },
      {
        "key": "start",
        "label": "Start coordinate, optional",
        "value": "",
        "type": "text",
        "inputMode": "numeric",
        "maxLength": 6,
        "help": "Leave both coordinates empty for whole records, or enter one-based inclusive coordinates. Gaps count as positions."
      },
      {
        "key": "end",
        "label": "End coordinate, optional",
        "value": "",
        "type": "text",
        "inputMode": "numeric",
        "maxLength": 6,
        "help": "Both coordinates must fit every selected record. Source identifiers, full headers and sequence case are unchanged; FASTA lines wrap at 80 symbols."
      }
    ],
    "registrationFamily": "sequence-tools",
    "presentation": "metrics",
    "note": "Select complete FASTA records by exact identifier or extract the same one-based inclusive coordinate range from each selected record. Ranges cannot wrap or run beyond record boundaries. Alignment gaps count as positions. Output preserves the original identifier, full header and sequence case, with coordinates recorded separately in JSON and CSV. Existing annotations in a header are not recalculated after extraction. Runs locally without uploads or database lookup. Limit: 500000 combined input characters, 2000 records, 2000 validation issues, a 1000-symbol motif, 20000 matches and 10000000 symbol comparisons. Exceeding a limit rejects the complete report. Each export is limited to 3000000 characters; typed CSV allows 200000 values. Preview shows 200 rows. Processing stops after 10 seconds.",
    "inputMaxLength": 500000,
    "inputErrorCode": "SEQUENCE_INPUT",
    "example": {
      "input": ">sample unchanged description\nACGTrynACGT\n",
      "options": {
        "alphabet": "dna",
        "allowGaps": "false",
        "recordIds": "sample",
        "start": "",
        "end": ""
      }
    },
    "experience": {
      "automatic": false,
      "single": false,
      "inputMaxLength": 500000,
      "inputMode": "text",
      "label": "Your text",
      "placeholder": "Type or paste your input…",
      "help": "Up to 500,000 characters. Review the settings before running.",
      "helpParts": [
        "Up to 500,000 characters.",
        "Review the settings before running."
      ],
      "action": null
    },
    "mode": "explicit",
    "interactive": false
  },
  "execution": "Browser interface",
  "api": null,
  "browser_agent": {
    "supported": true,
    "name": "run_current_tool",
    "discovery": "WebMCP on the human page in a supporting browser",
    "verification": "See audit/API-AUDIT.md; availability is not verification"
  }
}

Page guide