Scomber Colias

interactive genome visualization of Scomber colias


i. General overview

When you open the website, you will be confronted with the JBrowse2 component, an open source platform for visualization and integration of biological data, with a default session prepared for visualization.

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You can manipulate the visualization to your liking and explore the data. You can search for a hypothetical gene by its name ( e.g: hoxa10) and clicking Return will direct the visualization to the selected gene.

WARNING: Remember that these gene names were predicted by best blast-p hit.

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You will notice that the reference sequence is displayed in a gray box labeled "Zoom in to see sequence". You can zoom in and out using the [Magnifier Glass] icon or the general controls (e.g.: control + mouse wheel).

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ii. Get gene information

When you have found the gene you are interested in (e.g.: hoxa10 ), you can click on the gene to get a pop-up window with relevant information about the gene.

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If you scroll down to the Subfeatures section, you will find all the isoforms of the gene you are interested in, in the coordinated forms indicated. In this section you can retrieve the CDS, protein, gene-with-intron, gene-with-10bp-intron, gene-with-500bp-up+down-stream, gene-with-500bp-up+down-stream-with-10bp-intron, and cDNA sequences and copy them as plain text or in HTML format.

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iii. Additional tools

Additionally, you might want to zoom-in in a portion of the genome, or even get a portion of the sequence, in that case you can click and highlight a region using the bp scale under the browse menu and select Zoom to Region or Get Sequence.

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Zoom to region: Zooms in on the highlighted region.

Get sequence: Displays a pop-up window with the highlighted sequence.

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In development: A blast search tool is being developed to complement the website.


Scomber Colias Genome by AGE@CIIMAR © 2020

This visualization is powered by JBrowse2. This webpage is optimised for Google Chrome and Safari browsers.