Search results for "distribution:Bio-Graphics GENE"
Bio::Graphics::Glyph::gene - A GFF3-compatible gene glyph
This glyph is used for drawing genes that may have alternatively-spliced transcripts. The various isoforms are stacked on top of each other and given a single label and description that apply to the entire stack. Each individual transcript's name is ...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Glyph::rainbow_gene - A GFF3-compatible gene glyph
This glyph is used for drawing genes that may have alternatively-spliced transcripts. The various isoforms are stacked on top of each other and given a single label and description that apply to the entire stack. Each individual transcript's name is ...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Glyph::decorated_gene - A GFF3-compatible gene glyph with protein decorations
This glyph has the same functionality as the Bio::Graphics::Glyph::gene glyph, but uses the Bio::Graphics::Glyph::decorated_transcript glyph instead of the Bio::Graphics::Glyph::processed_transcript glyph to draw transcripts. One usecase for the 'dec...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
frend.pl - Render a Bio::Graphics Feature File on the web
The frend.pl script is a thin front end around the Bio::Graphics module. It accepts a list of files containing sequence (protein, nucleotide) feature coordinates from the file(s) listed on the command line or on standard input, renders them, and prod...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Panel - Generate GD images of Bio::Seq objects
The Bio::Graphics::Panel class provides drawing and formatting services for any object that implements the Bio::SeqFeatureI interface, including Ace::Sequence::Feature and Das::Segment::Feature objects. It can be used to draw sequence annotations, ph...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Glyph - Base class for Bio::Graphics::Glyph objects
Bio::Graphics::Glyph is the base class for all glyph objects. Each glyph is a wrapper around an Bio:SeqFeatureI object, knows how to render itself on an Bio::Graphics::Panel, and has a variety of configuration variables. End developers will not ordin...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Feature - A simple feature object for use with Bio::Graphics::Panel
This is a simple Bio::SeqFeatureI-compliant object that is compatible with Bio::Graphics::Panel. With it you can create lightweight feature objects for drawing. All methods are as described in Bio::SeqFeatureI with the following additions: The new() ...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
feature_draw.pl - Render a Bio::Graphics Feature File
The feature_draw.pl script is a thin front end around the Bio::Graphics module. It accepts a list of files containing sequence (protein, nucleotide) feature coordinates from the file(s) listed on the command line or on standard input, renders them, a...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::FeatureFile - A set of Bio::Graphics features, stored in a file
The Bio::Graphics::FeatureFile module reads and parses files that describe sequence features and their renderings. It accepts both GFF format and a more human-friendly file format described below. Once a FeatureFile object has been initialized, you c...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Glyph::xyplot - The xyplot glyph
This glyph is used for drawing features that have a position on the genome and a numeric value. It can be used to represent gene prediction scores, motif-calling scores, percent similarity, microarray intensities, or other features that require a lin...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Glyph::decorated_transcript - draws processed transcript with protein decorations
This glyph extends the functionality of the Bio::Graphics::Glyph::processed_transcript glyph and allows to draw protein decorations (e.g., signal peptides, transmembrane domains, protein domains) on top of gene models. Currently, the glyph can draw d...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Glyph::heterogeneous_segments - The "heterogeneous_segments" glyph
This glyph acts like graded_segments but the bgcolor of each segment (sub-feature) can be individually set using the source field of the feature. Each segment type color is specified using the following nomenclature: -{source}_color => $color For exa...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC