Region Location

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changing the location of the genomic region can be done through several means.

direct coordinate entry

coordinates can be directly entered into the search box at the top of the genome browser page

Gylyphs direct coordinate entry.png

The format of direct coordinate entry is very flexible. The order of asm:: chrom: start end is arbitrary. Chromosomes are recognized by either starting with chr or ending in a single : suffix. Genome name is recognized by a double :: suffix. The minimum requirement is that a chromosome name (eg chr3:) is specified. Any numbers in the query are assumed to be the start and end, order is not important. If only a single number is found then current genome length is preserved and it is centered on this chromosome positon.

Examples of valid direct chromosome locations

  • HG19::chr21:34949407-34965611
  • chr21:34949407-34965611
  • chr21:34949407..34965611
  • chr21:34,949,407-34,965,611 [ UCSC genome browser style ]
  • chr21:34949407..34965611 HG19::
  • chr21 35965611 34949407 HG19::
  • chr13 34231851 35327476
  • chr13 3496500
  • hg19:: chr13 35000000
  • 3496500 chr12

searching for genomic annotation with keywords

The annotation tracks loaded into the current view can be searched for specific features via keyword searching. This can be searching for entrez genes, refseq, ensembl genes, mirBASE, gencode, mRNA or any other annotation track which has metadata. Entrez genes in the ZENBU system have been loaded with extensive metadata, so one can even search for terms like hemo, liver, amyloid, or even complex multiple keyword queries. Then simply click the feature you want to move the view to.

Searching by known gene symbols will find genes in the Entrez Gene track Glyphs feature-search-egr1.png

Searching by refseq identifiers will find refseq genes
Glyphs feature-search-refseq.png

Searching by keywords will search the metadata find related genes in the Entrez Gene track
Glyphs gene-search-metadata.jpg

navigation with buttons

Glyphs navigation buttons.png

Big arrows move the view left or right retaining about 20% of the visible region. The small arrows move the view retaining about 80% of the visible region.

Plus zooms the view in. Minus zooms the view out.

The large 'recycle' button will reload the region querying data from the server. The small recycle button simply redraws the display using the data currently cached on the user's computer.

The user can also change the display width of the genome browser to better fit their larger desktop screen monitor or their smaller smartphone or tablet device.

In addition this section of the interface displays the current genomic location in black, and the current position of the tracking line in red.

zooming into selection within a track

Any track within the genome browser allows for interactive user selection using a simple click-and-drag motion. After a selection is made one can zoom into that region by clicking the magnify Glyphs magnify widget.png button.

For example from this zoomed out region the user has selected a region of several genes

Glyphs selection for zoom1.png

and then after clicking the magnify button the view is now zoomed into what was previously the selection

Glyphs selection for zoom2.png

focusing view by selecting an annotation feature

For example from this zoomed out view

Glyphs selection for zoom1.png

the user could double click the gene named AP2A1 which would select that feature and then zoom into it.

Glyphs feature selection.png

re-centering the view

If a user double clicks in the background of any track, the view will be re-centered on that location, but retains the same zoom level.