CGI functions

This page details what each CGI does. Note this is not a complete list of all of our CGIs.

cartDump and cartReset

These two CGIs will dump and reset your cart, respectively. The cart is what allows the browser to keep track of which assembly, tracks, custom tracks, etc you are viewing even when you navigate away from a page. cartReset will clear your cart (button on hgGateway and hgTables). cartDump will allow you to view the contents of your cart, which can be useful for debugging.

hgBlat

Runs BLAT (main link in the top blue bar: http://genome.ucsc.edu/cgi-bin/hgBlat), which allows users to search the genome for particular DNA, RNA or protein sequence(s).

hgc

Gives details about a specific item in a track when an item is clicked on. Runs the detail pages for all tracks except UCSC Genes and UCSC Gene-like tracks (e.g. FlyBase Genes).

hgConvert

Allows users to convert current genome coordinates between assemblies. To access it, click on the "Convert" link in the top blue bar when browsing an assembly.

hgCustom

Allows users to add custom tracks to the browser (http://genome.ucsc.edu/cgi-bin/hgCustom).

hgEncodeVocab

After clicking on the metadata "arrow" links on the hgTrackUi page, some of the terms in the metadata are linked to pages describing them. This CGI makes these links.

hgFileSearch

Runs File Search for ENCODE tracks.

hgFileUi

Allows users to interact with the downloads page for certain ENCODE tracks to find files of interest.

hgGateway

Runs the gateway page (click on genomes in the top blue bar: http://genome.ucsc.edu/cgi-bin/hgGateway), which allows users to choose which assembly they would like to view (hg19, for example).

hgGene

The details page for UCSC Genes and UCSC Gene-like tracks. You can reach this CGI by clicking on an item in the UCSC Genes track.

hgGenome

Runs Genome Graphs (main link in side blue bar from main page: http://genome.ucsc.edu/cgi-bin/hgGenome), which allows users to see the distribution of the items in a data set over the whole genome.

hgLiftOver

To get to hgLiftOver, go to Home -> Utilities -> Batch Coordinate Conversion (liftOver): http://genome.ucsc.edu/cgi-bin/hgLiftOver. Allows users to convert genome coordinates and genome annotation files between assemblies.

hgNear

Runs the Gene sorter (main link in the top blue bar: http://genome.ucsc.edu/cgi-bin/hgNear), which allows users to see how genes are related by various criteria.

hgPal

Shows protein alignments between species. There are 3 ways to get to the hgPal CGI:

1. "Protein FASTA" click-through from a UCSC Gene details page
2. "CDS FASTA" click-through from a RefSeq Genes details page
3. using the Table Browser, choose "CDS FASTA" as the output format (this should work for any genePred track)

hgPcr

Runs In-Silico PCR (main link in the top blue bar: http://genome.ucsc.edu/cgi-bin/hgPcr), which allows users to see what their PCR product would be given a set of primers.

hgSession

Runs Sessions (main link in the top blue bar: http://genome.ucsc.edu/cgi-bin/hgSession), which allows users to configure the browser with specific track combinations, including custom tracks, and save the configuration options.

hgTables

Runs the Table Browser (main link in the top blue bar: http://genome.ucsc.edu/cgi-bin/hgTables), which allows users to retrieve the data associated with a track in text format, to calculate intersections between tracks, and to retrieve DNA sequence covered by a track.

hgTracks

Runs the main browser, allowing users to view items in tracks. Also includes track search. http://genome.ucsc.edu/cgi-bin/hgTracks

hgTrackUi

You can get to this CGI by either clicking on the thin rectangle button to the right of the browser image or on the track name itself. Allows users to configure the track display options and, occasionally, the details displayed by hgc.

hgVisigene

Runs Visigene (main link in top blue bar from home page: http://genome.ucsc.edu/cgi-bin/hgVisiGene), which is a virtual microscope for viewing in situ images.

pbGateway, pbGlobal and pbTracks

Runs our Proteome browser (main link in the top blue bar), which allows users look at properties of proteins including sequence, polarity, etc.

phyloGif

Runs the Phylogenetic Tree Gif Maker, which creates a gif image from the phylogenetic tree specification given. To get to phyloGif, go to Home -> Utilities -> Phylogenetic Tree Gif Maker: http://genome.ucsc.edu/cgi-bin/phyloGif.