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== Selecting a genome to view == | |||
Gene pages in EcoliWiki have links that will take you to the appropriate view in Gbrowse. To change the genome being viewed while you are in Gbrowse, use the Data source menu. | |||
[[File:Gbrowse_data_source_menu.png|thumb|center|300px]] | |||
Contact us if there is a genome that you would like to see in the browser. | |||
==Finding a particular gene or region== | ==Finding a particular gene or region== | ||
To direct Gbrowse to a particular region of the chromosome, type a gene name, a short sequence (minimum of 15 bp), or a nucleotide range in the '''Landmark or Region''' box located near the top left of the page and click on the '''Search''' button. | === Using search === | ||
To direct Gbrowse to a particular region of the chromosome, type a gene name, a short sequence (minimum of 15 bp), or a nucleotide range in the '''Landmark or Region''' box located near the top left of the page and click on the '''Search''' button. Gbrowse will recognize a standard gene name as well as its synonyms. For example, in the MG1655 browser you can search for b numbers by typing bxxxx. | |||
Gbrowse will | To find a nucleotide range, type: <accession>:xx..yy, where | ||
* <accession> is the accession of the genome you are looking at. This will usually already be in the search box from the last thing you navigated to. | |||
* xx and yy indicate the nucleotide positions of the start and end of the range you want | |||
=== "Rubber band" selection === | |||
A convenient way to move along the genome is to click and drag in either the overview or region panels. Gbrowse will reload the image to encompass selected area when you release the mouse buttong | |||
=== Sliding handles === | |||
The area shown in the Details panel is highlighted by a box in the Overview and Region panels. You can grab the box and slide it left or right within limits (it can't slide over the whole genome). | |||
=== Scroll/Zoom === | |||
Once you get to a particular location, you can fine-tune the view the '''Scroll/Zoom''' buttons to move along the chromosome or change magnification. | |||
[[File:Gbrowse navigation.png |thumb|center|600px]] | |||
==Information displayed in Gbrowse== | ==Information displayed in Gbrowse== | ||
The information in Gbrowse is displayed in tracks, as shown in the image below. | The information in Gbrowse is displayed in tracks, as shown in the image below. | ||
*'''Overview''' is a linear display of the entire genome with | *'''Overview''' is a linear display of the entire genome with two dotted lines marking the location of the region being viewed. | ||
*'''Region''' displays | *'''Region''' displays 400 kb on either side of the position being viewed. This can change w/ scale. | ||
*The '''Details''' section displays more detailed information on genes in the region and contains multiple tracks. The user can set which of the tracks are shown. The image below has the tracks that show gene names ('''Genes'''), gene names and a brief description of gene product function ('''GenesDetail'''), '''Noncoding RNAs''', and the known or predicted operons ('''operon_RegulonDB'''). | *The '''Details''' section displays more detailed information on genes in the region and contains multiple tracks. The user can set which of the tracks are shown. The image below has the tracks that show gene names ('''Genes'''), gene names and a brief description of gene product function ('''GenesDetail'''), '''Noncoding RNAs''', and the known or predicted operons ('''operon_RegulonDB'''). | ||
[[ | [[File:Gbrowse_for_ecoliwiki.jpeg|thumb|center|600px]] | ||
*The '''Genes''' track contains link to other databases. To see the links, move the cursor over the bar representing the gene. | *The '''Genes''' track contains link to other databases. To see the links, move the cursor over the bar representing the gene. | ||
[[ | [[File:GBrowse_update2.jpg|center|600px]] | ||
*To set which tracks are shown, scroll to the '''Tracks''' display near the bottom of the page. Click the tracks you want displayed and click on the '''Update Image''' button. Each of the tracks has display options that can be set by clicking the '''Configure tracks''' button. | *To set which tracks are shown, scroll to the '''Tracks''' display near the bottom of the page. Click the tracks you want displayed and click on the '''Update Image''' button. Each of the tracks has display options that can be set by clicking the '''Configure tracks''' button. | ||
| Line 26: | Line 37: | ||
[[Image:Gbrowse_possible_tracks.jpg|thumb|center|600px]] | [[Image:Gbrowse_possible_tracks.jpg|thumb|center|600px]] | ||
== | == See also == | ||
=== Genome-specific information === | |||
* [[Help:Gbrowse/MG1655]] | |||
=== Additional functionalities === | |||
* [[Help:Gbrowse/Uploading_user_data_to_EcoliWiki_Gbrowse|Uploading private data]] | |||
* [[Help:Gbrowse/PCR primers|PCR primers]] | |||
[[Category:Help|Gbrowse]] | [[Category:Help|Gbrowse]] | ||
Latest revision as of 22:01, 24 May 2012
Selecting a genome to view
Gene pages in EcoliWiki have links that will take you to the appropriate view in Gbrowse. To change the genome being viewed while you are in Gbrowse, use the Data source menu.
Contact us if there is a genome that you would like to see in the browser.
Finding a particular gene or region
Using search
To direct Gbrowse to a particular region of the chromosome, type a gene name, a short sequence (minimum of 15 bp), or a nucleotide range in the Landmark or Region box located near the top left of the page and click on the Search button. Gbrowse will recognize a standard gene name as well as its synonyms. For example, in the MG1655 browser you can search for b numbers by typing bxxxx.
To find a nucleotide range, type: <accession>:xx..yy, where
- <accession> is the accession of the genome you are looking at. This will usually already be in the search box from the last thing you navigated to.
- xx and yy indicate the nucleotide positions of the start and end of the range you want
"Rubber band" selection
A convenient way to move along the genome is to click and drag in either the overview or region panels. Gbrowse will reload the image to encompass selected area when you release the mouse buttong
Sliding handles
The area shown in the Details panel is highlighted by a box in the Overview and Region panels. You can grab the box and slide it left or right within limits (it can't slide over the whole genome).
Scroll/Zoom
Once you get to a particular location, you can fine-tune the view the Scroll/Zoom buttons to move along the chromosome or change magnification.
Information displayed in Gbrowse
The information in Gbrowse is displayed in tracks, as shown in the image below.
- Overview is a linear display of the entire genome with two dotted lines marking the location of the region being viewed.
- Region displays 400 kb on either side of the position being viewed. This can change w/ scale.
- The Details section displays more detailed information on genes in the region and contains multiple tracks. The user can set which of the tracks are shown. The image below has the tracks that show gene names (Genes), gene names and a brief description of gene product function (GenesDetail), Noncoding RNAs, and the known or predicted operons (operon_RegulonDB).
- The Genes track contains link to other databases. To see the links, move the cursor over the bar representing the gene.
- To set which tracks are shown, scroll to the Tracks display near the bottom of the page. Click the tracks you want displayed and click on the Update Image button. Each of the tracks has display options that can be set by clicking the Configure tracks button.
