CGI functions: Difference between revisions
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===cartDump and cartReset=== | ===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. | 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=== | ===hgBlat=== | ||
Runs BLAT (main link in the top blue bar), which allows users to search the genome for particular DNA, RNA or protein sequence(s). | 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=== | ===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 ( | 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=== | ===hgConvert=== | ||
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===hgCustom=== | ===hgCustom=== | ||
Allows users to add custom tracks to the browser. | Allows users to add custom tracks to the browser (http://genome.ucsc.edu/cgi-bin/hgCustom). | ||
===hgEncodeVocab=== | ===hgEncodeVocab=== | ||
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===hgGateway=== | ===hgGateway=== | ||
Runs the gateway page (click on genomes in the top blue bar), which allows users to choose which assembly they would like to view (hg19, for example). | 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=== | ===hgGene=== | ||
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===hgGenome=== | ===hgGenome=== | ||
Runs Genome Graphs (main link in side blue bar from main page), which allows users to see the distribution of the items in a | 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=== | ===hgLiftOver=== | ||
To get to hgLiftOver, go to Home -> Utilities -> Batch Coordinate Conversion (liftOver). Allows users to convert genome coordinates and genome annotation files between assemblies. | 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=== | ===hgNear=== | ||
Runs the Gene sorter (main link in the top blue bar), which allows users to see | 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=== | ===hgPal=== | ||
Shows protein alignments between species. There are 3 ways to get to the hgPal CGI: | Shows protein alignments between species. There are 3 ways to get to the hgPal CGI: | ||
# | # "Protein FASTA" click-through from a UCSC Gene details page | ||
# | # "CDS FASTA" click-through from a RefSeq Genes details page | ||
# using the Table Browser, choose "CDS FASTA" as the output format (this should work for any genePred track) | # using the Table Browser, choose "CDS FASTA" as the output format (this should work for any genePred track) | ||
===hgPcr=== | ===hgPcr=== | ||
Runs In-Silico PCR (main link in the top blue bar), which allows users to see what their PCR product would be given a set of primers. | 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=== | ===hgSession=== | ||
Runs Sessions (main link in the top blue bar), which allows users to configure the browser with specific track combinations, including custom tracks, and save the configuration options. | 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. | ||
===hgSuggest=== | |||
The CGI that runs in the background when you type a gene name into the "gene" box (even though it seems like you're on hgGateway or hgTracks). http://genome.ucsc.edu/goldenPath/help/geneSearchBox.html | |||
===hgTables=== | ===hgTables=== | ||
Runs the Table Browser (main link in the top blue bar), 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. | 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=== | ===hgTracks=== | ||
Runs the main browser, allowing users to view items in tracks. Also includes track search. | Runs the main browser, allowing users to view items in tracks. Also includes track search. http://genome.ucsc.edu/cgi-bin/hgTracks | ||
===hgTrackUi=== | ===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. | 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=== | ===hgVisigene=== | ||
Runs Visigene (main link in top blue bar from home page), which is a virtual microscope for viewing in situ images. | 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=== | ===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. | Runs our Proteome browser (main link in the top blue bar), which allows users look at properties of proteins including sequence, polarity, etc. | ||
===phyloPng=== | |||
Runs the Phylogenetic Tree Gif Maker, which creates a gif image from the phylogenetic tree specification given. To get to phyloPng, go to Home -> Utilities -> Phylogenetic Tree Gif Maker: http://genome.ucsc.edu/cgi-bin/phyloPng. | |||
===hgUserSuggestion=== | |||
Provides a suggestion box for users, allowing them to submit ideas for browser improvements and receive automated confirmation. Users also receive a reference number they can use to follow up on their suggestion. http://genome.ucsc.edu/cgi-bin/hgUserSuggestion | |||
Latest revision as of 18:34, 14 June 2017
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:
- "Protein FASTA" click-through from a UCSC Gene details page
- "CDS FASTA" click-through from a RefSeq Genes details page
- 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.
hgSuggest
The CGI that runs in the background when you type a gene name into the "gene" box (even though it seems like you're on hgGateway or hgTracks). http://genome.ucsc.edu/goldenPath/help/geneSearchBox.html
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.
phyloPng
Runs the Phylogenetic Tree Gif Maker, which creates a gif image from the phylogenetic tree specification given. To get to phyloPng, go to Home -> Utilities -> Phylogenetic Tree Gif Maker: http://genome.ucsc.edu/cgi-bin/phyloPng.
hgUserSuggestion
Provides a suggestion box for users, allowing them to submit ideas for browser improvements and receive automated confirmation. Users also receive a reference number they can use to follow up on their suggestion. http://genome.ucsc.edu/cgi-bin/hgUserSuggestion
