[Genome] use of the shortmatch track through an url

[Heather Trumbower]

Hi Robert:

The genome browser URL recognizes a good number of key/value pairs.
To open to a particular database and region, you use db= and position=.
For example:

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg17&position=chr22:15000000-16000000

You can also control the visibility of any track.   The value is simply 
'full', 'pack', 'squish', 'dense' or 'hide'.  The key can be found by 
looking at the track label (it is a link to the hgTrackUi configuration 
page) or by doing http://genome.ucsc.edu/cgi-bin/cartDump.

The key for the Short Match track is oligoMatch.

So now your URL looks like:

http://genome.ucsc.edu/cgi-bin/hgTracks?oligoMatch=full&db=hg17&position=chr22:15000000-16000000

The last thing you would want to set is the search string.   We keep that 
in the key hgt.oligoMatch:

http://genome.ucsc.edu/cgi-bin/hgTracks?hgt.oligoMatch=ccccc&oligoMatch=full&db=hg17&position=chr22:15000000-16000000

I hope this is what you are looking for, let us know if you have further 
questions.

Heather Trumbower
UCSC Genome Bioinformatics Group


  On Tue, 3 Jul 2007, Robert Castelo wrote:

> dear people at ucsc,
>
> i'd like to ask you if it is possible to use the Short Match track under
> the Mapping and Sequencing Tracks directly through an url such that i
> can build a link which, when i click on it, opens the genome browser on
> a particular region of the genome and showing the perfect matches to
> some short sequence of my interest (i.e., the short sequence would have
> to go written on the url somehow..)
>
> i know this could be worked out through a custom track but i was
> wondering whether the Short Match would do this job also for me.
>
>
> thanks!!
>
> robert.
>
>