genome browser

100%

genome browser

✓ Published0🌍 Public

Last edited Apr 19, 2016

Created on Apr 19, 2016

This interactive genome browser visualizes gene arrangements across multiple phage genomes, comparing the positions of homologous genes. The visualization uses D3.js with SVG and animation to display genomic data loaded from a JSON file, with genes rendered as directional blocks along a horizontal track, colored by pham family. Each gene is clickable, linking to its sequence on PhagesDB, and hovering reveals a tooltip with details like gene name, pham, and coordinates. Toggles in the sidebar let users filter which genomes to display, enabling quick comparison of gene order and orientation between closely related phages like Butterscotch and PBl1.

AI-generated description

Genome browser for phamerator.org

forked from <a href='http://bl.ocks.org/scresawn/'>scresawn</a>'s block: <a href='http://bl.ocks.org/scresawn/b8a8fcb885b6840bfde5'>genome browser</a>

forked from <a href='http://bl.ocks.org/BDAguila/'>BDAguila</a>'s block: <a href='http://bl.ocks.org/BDAguila/42f1c37f325999025db3'>genome browser</a>

forked from <a href='http://bl.ocks.org/ericamartel/'>ericamartel</a>'s block: <a href='http://bl.ocks.org/ericamartel/cc6cd97c95a80f35c824cc24a5bf0f6d'>genome browser</a>

forked from <a href='http://bl.ocks.org/anonymous/'>anonymous</a>'s block: <a href='http://bl.ocks.org/anonymous/2e1f2a94cd49a429cda6d5a3d77e5271'>genome browser</a>

forked from <a href='http://bl.ocks.org/BrandonStroud/'>BrandonStroud</a>'s block: <a href='http://bl.ocks.org/BrandonStroud/33881b1947efe610b0e743580af093f8'>genome browser</a>

forked from <a href='http://bl.ocks.org/anonymous/'>anonymous</a>'s block: <a href='http://bl.ocks.org/anonymous/3f6b48f9c5d72fb14fafc28ed3129a9f'>genome browser</a>

Similar vizzes

Loading thumbnail…

genome browser

A genome browser displays multiple phage genomes side-by-side, showing genes as colored rectangles above and below a central ruler. Genes are colored by orientation, with tick marks and labels marking genomic positions at 100, 500, and 1000 base-pair intervals. The visualization uses D3.js to load JSON data, append SVG elements, and animate opacity transitions for the ruler, ticks, and gene blocks, with tooltips on hover.

MMorganShannonMaryBioInformatics

90% match

Loading thumbnail…

genome browser

This visualization presents a linear genome browser for phage genes, displaying four annotated genes along a 7,800-base-pair sequence. It shows the data before explaining the mechanics: a horizontal track with tick marks at 100, 500, and 1,000-base intervals, while gene blocks are drawn above or below the central axis based on their direction. The code uses D3.js (v3.5) with SVG elements and transitions to animate gene rectangles and labels, which fade in sequentially with staggered delays. Gene coordinates and strand information come from an external JSON file, with tick generation and placement driven by iterative data checks.

BBrandonStroud

89% match

Loading thumbnail…

genome browser

This interactive genome browser visualizes two phage genomes, U2 and L5, as horizontal tracks with genes drawn as directional blocks along each genome. Built with D3.js and SVG, it uses a tooltip to display the DNA sequence of each gene on hover, while checkboxes allow users to filter genes by phamily. The genome length is used to scale the track width, and gene positions are mapped from start/stop coordinates, with arrowheads indicating forward or reverse direction.

BBrandonStroud

89% match

Loading thumbnail…

genome browser for group project

This genome browser displays multiple phage genomes as horizontal tracks, each annotated with gene blocks indicating their position, length, and direction along a ruler with tick marks. The linked data, loaded from a JSON file using `d3.json`, contains genome lengths and gene coordinates for several phages. The visualization uses D3 for SVG rendering and animation, with `transition()` calls that fade in the ruler, tick marks, and gene rectangles over time. Gene direction is depicted by their placement above or below the central axis.

MMorganShannonMaryBioInformatics

87% match

Loading thumbnail…

genome browser

This genome browser visualizes gene annotations along a linear genome, using an animated D3.js layout to reveal gene positions, directions, and associated pham identifiers. The example loads gene data from a JSON file and renders each gene as a colored rectangle—green for forward direction and red for reverse—on a track with tick marks every 1000 bases. The initial view places genes off-screen, then transitions them into position over 1.5 seconds, with gene and pham labels fading in afterward. The code uses D3's `selection.transition` for animations and SVG for rendering, with tick marks generated from computed genome positions.

BBrandonStroud

84% match

Loading thumbnail…

The genome browser making multiples)

This interactive genome browser visualizes phage gene annotations along a linear genomic ruler. Each gene is rendered as an orange rectangle, with forward and reverse genes positioned on alternating tracks above and below a central axis to reduce overlap. The SVG animation reveals the ruler by fading in its stroke, while hover tooltips display gene names. The x-axis is scaled by sequence position, and tick marks at 100, 500, and 1000 base-pair intervals provide a genomic coordinate reference.

AAdamBlaine1

84% match

Loading thumbnail…

The genome browser

This visualization presents a genome browser that displays gene sequences along a linear genome track, with forward and reverse genes color-coded in green and red. It shows how genes are positioned and oriented within a genome, with tick marks marking 100, 500, and 1000 base-pair intervals. The view animates gene rectangles from an initial off-track position into their correct places along the track, while labels for gene names and phage numbers fade in sequentially. The code uses D3.js (version 3.5.5) to bind JSON data, manipulate SVG elements, and apply transitions.

AAdamBlaine1

82% match

Loading thumbnail…

genome browser

This interactive genome browser visualizes gene positions along a linear genome sequence, with genes displayed as colored blocks above and below a central axis based on their direction. The view animates gene rectangles growing into place, followed by staggered tick marks at 100, 500, and 1000 base-pair intervals. Using D3.js, the code loads gene data from a JSON file and applies chained transitions (`.transition().duration()`) to reveal elements sequentially, while fill colors encode forward (purple) or reverse (orange) strand orientation. The SVG canvas is sized proportionally to genome length, and tick marks fade or slide in at different speeds to build the final annotation.

BBrandonStroud

82% match