DOTTER:(1) General Commands Manual DOTTER:(1)NAME
dotter - Sequence dotplots with image enhancement tools.
SYNOPSIS
dotter [options] <horizontal_sequence> <vertical_sequence> [X options]
DESCRIPTION
Reference: Sonnhammer ELL & Durbin R (1995). A dot-matrix program with dynamic threshold control suited for genomic DNA and protein
sequence analysis. Gene 167(2):GC1-10.
Allowed types:
Protein - Protein DNA - DNA DNA - Protein
Options:
-b <file>
Batch mode, write dotplot to <file>
-l <file>
Load dotplot from <file>
-m <float>
Memory usage limit in Mb (default 0.5)
-z <int>
Set zoom (compression) factor
-p <int>
Set pixel factor manually (ratio pixelvalue/score)
-W <int>
Set sliding window size. (K => Karlin/Altschul estimate)
-M <file>
Read in score matrix from <file> (Blast format; Default: Blosum62).
-F <file>
Read in sequences and data from <file> (replaces sequencefiles).
-f <file>
Read feature segments from <file>
-H Do not calculate dotplot at startup.
-R Reversed Greyramp tool at start.
-r Reverse and complement horizontal_sequence (DNA vs Protein)
-D Don't display mirror image in self comparisons
-w For DNA: horizontal_sequence top strand only (Watson)
-c For DNA: horizontal_sequence bottom strand only (Crick)
-q <int>
Horizontal_sequence offset
-s <int>
Vertical_sequence offset
Some X options: -acefont <font> Main font. -font <font> Menu font.
SEE ALSO
http://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html for more info.
AUTHOR
Erik.Sonnhammer@cgb.ki.se Version 3.1, compiled Jul 10 2010
July 2010 DOTTER:(1)
Check Out this Related Man Page
Bio::Graphics::Glyph::generic(3pm) User Contributed Perl Documentation Bio::Graphics::Glyph::generic(3pm)NAME
Bio::Graphics::Glyph::generic - The "generic" glyph
SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
DESCRIPTION
This is identical to the "box" glyph except that it will draw the subparts of features that contain subfeatures. The subparts are not
connected -- use the "segments" glyph for that. "Generic" is the default glyph used when not otherwise specified.
METHODS
This module overrides the maxdepth() method to return 0 unless the -maxdepth option is provided explicitly. This means that any module that
inherits from generic will need to override maxdepth() again in order to draw subfeatures. In general, those implementing multi-segmented
feature glyphs should inherit from Bio::Graphics::Glyph::segments, which allows for one level of descent.
In addition, the following new methods are implemented:
labelfont(), descfont(), labelwidth(), descriptionwidth()
Return the font, width for the label or description.
label()
Return the glyph label text (printed above the glyph).
description()
Return the glyph description text (printed below the glyph).
draw_translation()
Draw the protein translation of the feature (assumes that the feature is attached to a DNA sequence).
draw_sequence()
Draw the sequence of the feature (either DNA or protein).
OPTIONS
The following options are standard among all Glyphs. See Bio::Graphics::Glyph for a full explanation.
Option Description Default
------------------------
-fgcolor Foreground color black
-bgcolor Background color turquoise
-fillcolor Synonym for -bgcolor
-linewidth Line width 1
-height Height of glyph 10
-font Default font gdSmallFont
-label_font Font used for label gdSmallFont
-desc_font Font used for description gdSmallFont
-connector Connector type 0 (false)
-connector_color
Connector color black
-pad_top Top padding 0
-pad_bottom Bottom padding 0
-label Whether to draw a label 0 (false)
-label_position Where to draw the label "top" (default) or "left"
-description Whether to draw a description 0 (false)
-strand_arrow Whether to indicate 0 (false)
strandedness
-hilite Highlight color undef (no color)
-draw_dna If true, draw the dna residues 0 (false)
when magnification level
allows.
-canonical_strand If true, draw the dna residues 0 (false)
as they appear on the plus strand
even if the feature is on the minus
strand.
-pad_top and -pad_bottom allow you to insert some blank space between the glyph's boundary and its contents. This is useful if you are
changing the glyph's height dynamically based on its feature's score.
BUGS
Please report them.
SEE ALSO
Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Glyph::arrow, Bio::Graphics::Glyph::cds, Bio::Graphics::Glyph::crossbox,
Bio::Graphics::Glyph::diamond, Bio::Graphics::Glyph::dna, Bio::Graphics::Glyph::dot, Bio::Graphics::Glyph::ellipse,
Bio::Graphics::Glyph::extending_arrow, Bio::Graphics::Glyph::generic, Bio::Graphics::Glyph::graded_segments,
Bio::Graphics::Glyph::heterogeneous_segments, Bio::Graphics::Glyph::line, Bio::Graphics::Glyph::pinsertion, Bio::Graphics::Glyph::primers,
Bio::Graphics::Glyph::rndrect, Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::ruler_arrow, Bio::Graphics::Glyph::toomany,
Bio::Graphics::Glyph::transcript, Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::translation, Bio::Graphics::Glyph::triangle,
Bio::Graphics::Glyph::xyplot, Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD
AUTHOR
Allen Day <day@cshl.org>, Lincoln Stein <lincoln.stein@gmail.com>
Copyright (c) 2001 Cold Spring Harbor Laboratory Copyright (c) 2010 Ontario Institute for Cancer Research
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
perl v5.14.2 2012-02-20 Bio::Graphics::Glyph::generic(3pm)