Obscure But Useful Browser Features

The alternating blue and grey buttons (a.k.a. mini-buttons) 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 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 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 coloured 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 colour.

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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 hg18 and use the following url: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=%s (as you can see, position is replaced with %s). When you type "hg18 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.

hg18 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.cse.ucsc.edu/cgi-bin/hgTracks?db=canFam2&position=%s