Ucsc Genome Tools

Configuration File: ucsc_genome_tools.json Tool Type: Local Tools Count: 4

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_list_tracks (Type: UCSCGenomeTool)

Discover available UCSC Genome Browser annotation tracks for a genome assembly, and inspect a tra…

UCSC_list_tracks tool specification

Tool Information:

  • Name: UCSC_list_tracks

  • Type: UCSCGenomeTool

  • Description: Discover available UCSC Genome Browser annotation tracks for a genome assembly, and inspect a track’s column schema. With only ‘genome’ set, returns the list of leaf tracks (each with track name, type, shortLabel, longLabel, parent) so you can find valid track names to pass to UCSC_get_track (there are tens of thousands, e.g. dbSnp155, dbSnp155ClinVar, dbSnp155Common, knownGene, ncbiRefSeq, encodeCcreCombined). Use ‘name_filter’ to narrow the list by substring (matched against track name, shortLabel, longLabel). When ‘track’ is also provided, returns that track’s column schema instead (column name, sqlType, jsonType, description) from the list/schema endpoint. Example: genome ‘hg38’ returns 23000+ tracks; genome ‘hg38’ + track ‘knownGene’ returns its 27 columns (chrom, chromStart, …).

Parameters:

  • genome (string) (required) UCSC genome assembly identifier. Examples: ‘hg38’, ‘hg19’, ‘mm39’, ‘mm10’, ‘dm6’, ‘danRer11’.

  • track ([‘string’, ‘null’]) (optional) Optional. When set, return this track’s column schema instead of the track list. Example: ‘knownGene’, ‘dbSnp155’, ‘ncbiRefSeq’.

  • name_filter ([‘string’, ‘null’]) (optional) Optional substring filter (case-insensitive) applied to track name/shortLabel/longLabel when listing tracks. Example: ‘dbSnp’, ‘gencode’, ‘clinvar’.

  • max_tracks ([‘integer’, ‘null’]) (optional) Maximum number of tracks to return when listing (default 500). The total matched count is always reported in track_count.

Example Usage:

query = {
    "name": "UCSC_list_tracks",
    "arguments": {
        "genome": "example_value"
    }
}
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)