Querying the Genome Browser

From the Genomes page, you can jump to the default position of an assembly by clicking the "Go" button or you can specify a particular genome position in a variety of formats. These same formats are valid in the search bar above the main Genome Browser track display.

Valid position queries can include:

To specify a genome position:

  1. Select the desired clade, genome and assembly
  2. Enter the desired query in the "Position/Search Term" box (see sample queries below)
  3. Click the "Go" button

Note: A query may have multiple results. If this is the case, a results page will appear listing each result along with the track it is associated with. Once selected, the result will be displayed in the Browser with a highlighted tag, making it easier to identify. Also, if you have further questions, you can search the Genome Browser FAQ page and find links to further resources. Also, developers of track hubs can create searchable track hubs using the searchTrix setting.

Sample queries

Below is a list of examples that might be used to query the Genome Browser. Note that not every query listed here will produce a result in every assembly. The list serves only to illustrate the different types of queries that can be performed.

QueryGenome Browser Response
chr7 Displays all of chromosome 7
chr3:1-1000000 Displays the first million bases of chromosome 3, counting from the p-arm telomere
3:1-1000000 Displays the first million bases of chromosome 3, Ensembl format chromosome names
chr3 0 1000000 Displays the first million bases of chromosome 3; BED format
NC_000007.14:1-1000000 Displays the first million bases of chromosome 3, RefSeq format
CM000665.2:1-1000000 Displays the first million bases of chromosome 3, GenBank/INSDC format
chr3:1000000+2000 Displays a region of chromosome 3 that spans 2000 bases, starting with position 1000000
chrUn_GL000213v1 Displays all of the unplaced contig GL000213v1
chr3_GL000221v1_random Displays the unlocalized contig GL000221v1
chr1_KN196472v1_fix Displays all of patch fix KN196472v1
20p13 Displays the region for band p13 on chromosome 20
GTATGTAGCCACGGAGCACCATTACCTGTCACCATTACCTGAATGGCTA Displays the first best match to this DNA sequence, e.g. chr21:33034835-33034883 for hg19
AA205474 Displays the region containing the EST with GenBank accession AA205474 in the BRCA1 cancer gene on chromosome 17
AC008101 Displays the region containing the clone with GenBank accession AC008101
AF083811 Displays the region containing the mRNA with GenBank accession number AF083811
NM_017414 Displays the region containing RefSeq identifier NM_017414
NP_059110 Displays the region containing protein accession number NP_059110
PRNP Displays the region containing HUGO Gene Nomenclature Committee identifier PRNP
Q99697 Displays the region containing the alignment of the UniProt/SwissProt protein sequence with accession Q99697 (PITX2)
Displays the region between genome landmarks, such as the STS markers RH18061 and RH80175, or chromosome
bands 15q11 to 15q13, or SNPs NM_000310.4 and NM_012090.5. This syntax may also be used for other range queries,
such as between uniquely determined ESTs, mRNAs, refSeqs, SNPS, etc.
BRCA1 Ala744Cys
Displays the region that matches the HGVS expression, usually in the format <transcript or protein>:<position> <amino acid or nucleotide change>
If a gene symbol is used, HGVS search will try all RefSeq transcripts to find the nucleotide or amino acid at the position indicated in the expression. If there are multiple matches, a disambiguation page will be shown. If the RefSeq sequence differs from the genome sequence, then currently the search will use the genome, not the transcript, for codon counting and amino acid / nucleotide comparison. Please contact us if this is inconvenient.
essv8694097 Displays the region covering the copy number variant with the accession essv8694097 in the Database of Genomic Variants (DGV)
nssv3446126 Displays the region covering the copy number variant with the accession nssv3446126 in the cases of developmental delay
CTD-3071L10 Displays the region covering the CTD-3071L10 NCBI clone end mapping in the NCBI Clone DB database
nssv16167444 Displays the region covering the common copy number genomic variant with the accession nssv16167444 in the nstd186 (NCBI Curated Common Structural Variants) dataset
COSM6161404 Displays the region covering COSM6161404 in the Catalogue Of Somatic Mutations In Cancer (COSMIC) database
nssv3395351 Displays the region covering ClinVar Copy Number Variant with the accession nssv3395351 in the ClinVar database
BRCT_assoc Displays the region covering the manually-curated Pfam-A domain BRCT_assoc found in GENCODE Genes
U133A:219211_at Displays the region containing the consensus and exemplar sequences used for the selection of probes on the Affymetrix HG-U133A chips
chr1 0 1000 When entered without ":" and "-", uses 0-based, half-open coordinates (like custom tracks and internal table coordinates), so displays chr1:1-1000
pseudogene mRNA Lists transcribed pseudogenes, but not cDNAs
p53 Lists mRNAs related to the p53 tumor suppressor
T-cell receptor Lists mRNAs for T-cell receptor genes in GenBank
breast cancer Lists mRNAs associated with breast cancer
homeobox caudal Lists mRNAs for caudal homeobox genes
zinc finger Lists zinc finger mRNAs
kruppel zinc finger Lists only kruppel-like zinc fingers
huntington Lists candidate genes associated with Huntington's disease
zahler Lists mRNAs deposited by a scientist named Zahler
Evans,J.E. Lists mRNAs deposited by co-author J.E. Evans

Use this last format for author queries. Although GenBank requires the search format Evans JE, internally it uses the format Evans,J.E..