GeneD3

Interactive sequence comparisons in D3

Click the image above to see an interactive example of GeneD3:

• zoom and drag
• hover over blocks to see annotation (GenBank)
• click and hold comparisons to see alignment and identity (BLAST)

Usage

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geneD3.py --files Sequence1.gbk,Sequence2.gbk --names Seq1,Seq2

Output

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The program outputs the visualization as HTML, which can be opened in Chrome or Firefox.

SVG Crowbar can download the visualization as a static vector file, works in both Chrome and Firefox.

Dependencies

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• BLAST+

• Python 3

• Pandas

• BioPython

Installation

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git clone https://github.com/esteinig/geneD3.git $HOME/geneD3
chmod +x $HOME/geneD3/geneD3.py
echo "export PATH=$PATH:$HOME/geneD3" >> $HOME/.bashrc
source $HOME/.bashrc

Options

---

geneD3.py --help

Basics

--files           Comma-delimited list of annotation and sequence files, complete GenBank
--names           Comma-delimited list of unique names for each sequence
--features        Comma-delimited list of features to parse from annotation (CDS)
--qualifiers      Comma-delimited list of qualifiers to parse from annotations (gene,product)
--path            Project path (.)
--project         Name of project (GeneD3)
--write_segments  Write segment files to project path for manual manipulation,
                  e.g. colours or annotation tooltips (False)
--read_segments   Read segment files from project path, overrides previous
                  properties of segments (False)

BLAST

--blast_path      Path to blastn or blastp executable (blastn)
--makedb_path     Path to makeblastdb (makeblastdb)
--db_type         BLAST DB type, corresponding to executable (nucl)
--identity        Minimum identity to include comparison (0.80)
--length          Minimum alignment length to include comparison (1000)
--evalue          BLAST e-value (1e-06)

Visualization

--title                 Plot title (GeneD3)
--width                 Canvas width (1800)
--height                Canvas height (1200)
--scale                 Scale segments, default to width of canvas (1800)

--gap                   Gap between sequence segments (300)
--block_height          Height of segment blocks (50)
--block_colour          Base colour of segment blocks (darkgray)
--line_width            Width of sequence line (5)
--line_colour           Colour of sequence line (gray)
--polygon_gap           Gap between comparison polygon and segments (10)
--polygon_fill          Polygon colour (darkgray)
--polygon_opacity       Polygon opacity (0.8)
--polygon_line_colour   Polygon line colour (darkgray)
--polygon_line_width    Polygon line width (1)

Text

--title_colour          Title colour (#404040)
--title_opacity         Title opacity (0.8)
--title_font_family     Title font family (times)
--title_font_weight     Title font weight (bold)
--title_font_size       Title font size (400%)

--name_colour           Name colour (#404040)
--name_opacity          Name opacity (0.8)
--name_font_family      Name font family (times)
--name_font_weight      Name font weight (bold)
--name_font_size        Name font size (400%)

Coordinates

--y_start   Start of segments, Y (250)
--x_start   Start of segments, X (500)
--y_text    Segments names, relative to top of segments, Y (10)
--x_text    Segment names, X (0
--y_title   Title, Y (100)
--x_title   Title, defaults to half of canvas width X (900)

Update

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In the next version:

• pip install on PyPI
• tests and code annotations
• download accessions from NCBI
• forward / reverse marker style
• alignment of segments on canvas
• additional annotation and sequence formats
• polygon opacity or colour scaled by identity