Obscure But Useful Browser Features

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You may be able to speed up the browser display dramatically by turning off the track control buttons under the graphic display. Some WEB browsers (in particular, Mac Safari) seem to take forever figuring out how to arrange all those buttons. Go to the "Configure" page, and turn off the item: Show track controls under main graphic or use the 'collapse all' button to collapse the track groups.

Also on the Configure page, find the Next Item and Next exon arrows buttons. They help for navigating along a chromosome and add little arrows on the edge of the screen. They do not show up in PDF images made from the page.

The base position ruler track has some fascinating track controls to add titles and position information to the tracks gif image. An excellent aid for preparing presentation slides.

The small grey buttons or bars (a.k.a. mini-buttons or mini-bars) at the very left edge of the browser gif tracks display will open a page where you can adjust various parameters that control the display of the track. This is also the same function entered if you click on the text label above the track visibility control drop down list (hide, dense, pack, etc...).

The small arrow left arrow ---> or right arrow <--- displayed when the base position track is set to full visibility mode to the left of the track in the margin where track labels usually are, is used to reverse the direction of nucleotide display when the viewpoint is close enough. Thus you can view either the forward strand bases, or the reverse strand bases. Click directly on the arrow itself to reverse the display. The display always displays the 5' of the forward strand to the left in the tracks display.

The chain- and net- tracks are colored by chromosome. Keeping this in mind, you can easily spot locations of synteny, e.g., two features that are far apart but share the same color.

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This is not really browser-related but I don't know any other place to put it: In firefox, create a bookmark with the keyword hg19 and use the following url: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=%s (as you can see, position is replaced with %s). When you type "hg19 dach" into the firefox url bar and press return, this will directly jump to the gene...I'm using this all the time now, also for genecards and pubmed. (max)

hg19 is tedious to type so I make the keyword simply h for homSap and then type in the gene name eg h prnp. that makes it easy to move around to orthologs in various species, using d for canFam etc with firefox bookmark http://genome-test.soe.ucsc.edu/cgi-bin/hgTracks?db=canFam2&position=%s