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 genomic region. Pass ‘region’ as a written lo…
UCSC_get_sequence tool specification
Tool Information:
Name:
UCSC_get_sequenceType:
UCSCGenomeToolDescription: Get DNA sequence from the UCSC Genome Browser for a genomic region. Pass ‘region’ as a written locus (e.g. ‘chr14:89000000-89000100’, 1-based inclusive, 101 bp) to paste coordinates verbatim, or give chrom/start/end with ‘coordinate_system’. Returns the nucleotide sequence plus the resolved region in both conventions. Useful for primer design, sequence analysis and regulatory element inspection.
Parameters:
genome(string) (required) UCSC genome assembly identifier. Examples: ‘hg38’ (human), ‘mm39’ (mouse), ‘dm6’ (fly), ‘sacCer3’ (yeast).chrom(string) (optional) Chromosome name. Examples: ‘chr1’, ‘chr17’, ‘chrX’, ‘chrM’.start(integer) (optional) Start position. Interpreted per ‘coordinate_system’ (default 0-based, inclusive). Example: 7668421.end(integer) (optional) End position. Exclusive when coordinate_system is 0-based, inclusive when 1-based. Span must be <= 100000 bp. Example: 7668521.region(string) (optional) Genomic region written the usual way, 1-based INCLUSIVE on both ends, e.g. ‘chr14:89000000-89000100’ (101 bp). This is the form shown by the UCSC browser, IGV and samtools, so you can paste a locus verbatim. PREFERRED over chrom/start/end: it removes the 0-based/1-based conversion that otherwise silently drops the first base.coordinate_system(string) (optional) Which convention chrom/start/end are given in. ‘0-based’ (default) is half-open, matching the UCSC API: length = end - start. ‘1-based’ is inclusive, matching a written locus: length = end - start + 1. Ignored when ‘region’ is supplied.
Example Usage:
query = {
"name": "UCSC_get_sequence",
"arguments": {
"genome": "example_value"
}
}
result = tu.run(query)
UCSC_get_track (Type: UCSCGenomeTool)#
Get annotation track data for a genomic region. If UCSC reports maxItemsLimit=true, the response …
UCSC_get_track tool specification
Tool Information:
Name:
UCSC_get_trackType:
UCSCGenomeToolDescription: Get annotation track data for a genomic region. If UCSC reports maxItemsLimit=true, the response sets truncated and includes a remediation note; UCSC supplies no continuation cursor, so increase maxItemsOutput or split the interval before treating results as complete.
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 UCSC Genome Browser tracks with exact track_count and recoverable local offset paginatio…
UCSC_list_tracks tool specification
Tool Information:
Name:
UCSC_list_tracksType:
UCSCGenomeToolDescription: Discover UCSC Genome Browser tracks with exact track_count and recoverable local offset pagination. Continue with next_offset while has_more is true. When track is provided, returns that track’s column schema instead of the list.
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.offset(integer) (optional) Zero-based offset in the filtered track list. Continue with next_offset.
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 the t…
UCSC_search tool specification
Tool Information:
Name:
UCSC_searchType:
UCSCGenomeToolDescription: Search the UCSC Genome Browser for genes, transcripts, or genomic features by name. Returns the true match count across all returned tracks with explicit local offset pagination; continue with next_offset while has_more is true. Supports gene symbols, transcript IDs, SNP rsIDs, and chromosomal bands.
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’.limit(integer) (optional) Maximum position matches per page (default 50, max 1000).offset(integer) (optional) Zero-based match offset. Continue with next_offset while has_more is true.
Example Usage:
query = {
"name": "UCSC_search",
"arguments": {
"search_term": "example_value"
}
}
result = tu.run(query)