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.

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
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
374180 Displays the region containing Entrez Gene identifier 374180
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
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 containing HGVS term
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..