Ucsc Genome Tools

Configuration File: ucsc_genome_tools.json Tool Type: Local Tools Count: 3

This page contains all tools defined in the ucsc_genome_tools.json configuration file.

Available Tools

UCSC_get_sequence (Type: UCSCGenomeTool)

Get DNA sequence from the UCSC Genome Browser for a specified genomic region. Returns the nucleot…

UCSC_get_sequence tool specification

Tool Information:

  • Name: UCSC_get_sequence

  • Type: UCSCGenomeTool

  • Description: Get DNA sequence from the UCSC Genome Browser for a specified genomic region. Returns the nucleotide sequence for a given chromosome, start, and end position in a genome assembly. Useful for primer design, sequence analysis, and regulatory element inspection. Example: hg38, chr17, start=7668421, end=7668521 returns 100bp of TP53 sequence.

Parameters:

  • genome (string) (required) UCSC genome assembly identifier. Examples: ‘hg38’ (human), ‘mm39’ (mouse), ‘dm6’ (fly), ‘sacCer3’ (yeast).

  • chrom (string) (required) Chromosome name. Examples: ‘chr1’, ‘chr17’, ‘chrX’, ‘chrM’.

  • start (integer) (required) 0-based start position (inclusive). Example: 7668421.

  • end (integer) (required) End position (exclusive). Must be > start and span <= 100000 bp. Example: 7668521.

Example Usage:

query = {
    "name": "UCSC_get_sequence",
    "arguments": {
        "genome": "example_value",
        "chrom": "example_value",
        "start": 10,
        "end": 10
    }
}
result = tu.run(query)

UCSC_get_track (Type: UCSCGenomeTool)

Get annotation track data from the UCSC Genome Browser for a specified genomic region. Retrieves …

UCSC_get_track tool specification

Tool Information:

  • Name: UCSC_get_track

  • Type: UCSCGenomeTool

  • Description: Get annotation track data from the UCSC Genome Browser for a specified genomic region. Retrieves features like genes, regulatory elements, conservation scores, variants, or repeats from any of UCSC’s 370+ tracks. Use UCSC_search first to find the genomic coordinates of your gene of interest. Example: track ‘knownGene’ on hg38 chr17:7668421-7687490 returns GENCODE gene annotations for the TP53 region.

Parameters:

  • genome (string) (required) UCSC genome assembly. Examples: ‘hg38’, ‘hg19’, ‘mm39’.

  • track (string) (required) Track name. Common tracks: ‘knownGene’ (GENCODE genes), ‘ncbiRefSeq’ (RefSeq), ‘snp151’ (dbSNP), ‘encodeCcreCombined’ (ENCODE cCREs), ‘phastCons100way’ (conservation), ‘rmsk’ (repeats).

  • chrom (string) (required) Chromosome name. Examples: ‘chr1’, ‘chr17’, ‘chrX’.

  • start (integer) (required) 0-based start position (inclusive).

  • end (integer) (required) End position (exclusive). Must be > start.

  • maxItemsOutput ([‘integer’, ‘null’]) (optional) Maximum number of items to return. Default: 100. Set to limit large result sets.

Example Usage:

query = {
    "name": "UCSC_get_track",
    "arguments": {
        "genome": "example_value",
        "track": "example_value",
        "chrom": "example_value",
        "start": 10,
        "end": 10
    }
}
result = tu.run(query)

UCSC_search (Type: UCSCGenomeTool)

Search the UCSC Genome Browser for genes, transcripts, or genomic features by name. Returns posit…

UCSC_search tool specification

Tool Information:

  • Name: UCSC_search

  • Type: UCSCGenomeTool

  • Description: Search the UCSC Genome Browser for genes, transcripts, or genomic features by name. Returns position matches across tracks (MANE, RefSeq, GENCODE, HGNC, etc.) for a given genome assembly. Supports searching for gene symbols, transcript IDs, SNP rsIDs, or chromosomal bands. Example: searching ‘TP53’ in hg38 returns chr17:7668421-7687490 from MANE Select and other tracks.

Parameters:

  • search_term (string) (required) Gene symbol, transcript ID, SNP rsID, or genomic feature to search. Examples: ‘TP53’, ‘BRCA1’, ‘rs429358’, ‘ENST00000269305’.

  • genome (string) (optional) UCSC genome assembly identifier. Default: ‘hg38’. Others: ‘hg19’, ‘mm10’, ‘mm39’, ‘dm6’, ‘ce11’, ‘danRer11’, ‘sacCer3’.

Example Usage:

query = {
    "name": "UCSC_search",
    "arguments": {
        "search_term": "example_value"
    }
}
result = tu.run(query)