A Macromolecule Schematic Drawing Program
Home

DomainDraw: Input Example
General Settings
Image width: pixels Increase the width of the image if the macromolecules being drawn are especially long or if macromolecules of very different lengths are being drawn on the same schematic. The maximum allowed width is 8000 pixels.
Font scale: 1 (recommended for image widths < 800 pixels
2
3 (recommended for image widths > 1200 pixels
The font scale allows larger fonts to be used if a large image is requested. The ideal scale for any given image is most likely determined by personal preference. Anti-aliasing will only be performed on Scale 1 fonts.
Legend type: Simple
Long
A simple legend will list the domains the occur in the schematic. A long legend will list each occurrence of each domain with the range of that domain. The long legend is useful when exact positional information is a crucial part of the diagram.
Bar color: The bar color defines the color of the rectangle that represents the macromolecule. It is the visual scaffold on which the domain and motifs are drawn.
Background color: Black is recommended for making slides, while white is a good choice for printed materials.
Output format: PNG is the output format recommended for web use, although JPG and GIF are also good options. PSD, TIFF, and PS are recommended for use in creating figures for publication or other non-web uses.
Motifs and Domains

Domains that have the same macromolecule name will be drawn on the same bar. In the case of domains that span overlapping regions, the domains will be drawn such that the color and range of each domain is visible.

Domains and motifs of different types will be drawn as different shapes. Here, domains or motifs that are defined by their functional role are drawn as rounded rectangles; domains or motifs that are characterized by their structural role are drawn as rectangles; domains or motifs that consist of a single residue or have an unknown range (but a starting position) are drawn as an asterisk.

The status of the validity of the domain is encoded by a colored border around the domain/motif shape drawn on the macromolecule bar.

If no domain or motif is selected to align multiple macromolecule schematics to, the macromolecule bars will be left-aligned with their first residue. If a domain is chosen to align macromolecule bars to, the last instance of that domain on a macromolecule bar is used to align all schematics.

Web form-based input:
Listed here are some sample domains.

Macromolecule
name
Motif name Position/Range Macromolecule
length (or range)
Motif type Method (optional) Motif validity status Motif color Align to motif
1 Functional
Structural
Predicted
Disproved
Confirmed
2 Functional
Structural
Predicted
Disproved
Confirmed
3 Functional
Structural
Predicted
Disproved
Confirmed
4 Functional
Structural
Predicted
Disproved
Confirmed
5 Functional
Structural
Predicted
Disproved
Confirmed


File-based input:
These are the domains as they would be entered in a file for input. An ampersand (&) is used a delimiter between the columns. White space before or after the delimiters is ignored. [Download this file]
CAA46951 & Homeobox domain & 192:248 & F & #CDC1C5 & NULL & PFAM & Y & 433 & 
CAA46951 & Homeodomain-like & 165:252 & S & #CD5B45 & NULL & SCOP & Y & 433 & 
5330400P12 & WD domain, G-beta repeat & 131:168 & F & #FF8C69 & NULL & PFAM & Y & 296 & 
5330400P12 & WD domain, G-beta repeat & 173:210 & F & #FF8C69 & NULL & PFAM & Y & 296 & 
5330400P12 & WD40-repeat & 1:296 & S & #00FF7F & NULL & SCOP & Y & 296 & 
AAH62206 & Cell division protein & 38:311 & S & #00CED1 & NULL & PFAM & Y & 425 & 
AAH62206 & P-loop containing nucleoside triphosphate hydrolases & 36:279 & S & #00FFFF & NULL & SCOP & Y & 425 & 
For uploaded input files, an additional feature is available: an imagemap file that links domain shapes with a URL. The desired URL is listed at the end of each domain entry in the input file. See the example below. [Download this file]
BAA88685 & Choline/Carnitine o-acyltransferase & 172:763 & F & #ADD8E6 & PF00755 & PFAM & Y & 772 & http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00755
BAA88685 & E set domains & 9:63 & S & #CD2626 & 81296 & SCOP & Y & 772 & http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?key=81296
BAA88685 & CoA-dependent acyltransferases & 168:542 & S & #CD6889 & 52777 & SCOP & Y & 772 & http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?key=52777
BAA88685 & CoA-dependent acyltransferases & 544:766 & S & #CD6889 & 52777 & SCOP & Y & 772 & http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?key=52777
Sometimes it is useful to display partial protein sequences or sections of DNA with respect to a transcriptional start site. In these cases, the range displayed at the start and end of the bar representing the molecule will not be 1 to N but rather -1000 to 10 or 200 to 500, for example. To support these cases, a range for the bar can be included in place of the length of the molecule and the format is the same as that used to describe the range of the domain (e.g., -1000:10). See the example below which represents predicted transcription factor binding sites in the upstream regulatory region of the IL-2 receptor alpha gene. [Download this file]
IL-2Ra & AML-1a & -548:-543 & S & #EFEFEF & NULL &  & R & -600:1 & 
IL-2Ra & CdxA & -500:-494 & S & #000000 & NULL &  & R & -600:1 & 
IL-2Ra & CdxA & -457:-451 & S & #000000 & NULL &  & R & -600:1 & 
IL-2Ra & CdxA & -235:-229 & S & #000000 & NULL &  & R & -600:1 &
DomainDraw: Output Example

The default general settings and the first input file described above were used to generate the following image:



Copyright 2004, 2005, 2006, Institute of Molecular Bioscience, The University of Queensland and the ARC Centre in Bioinformatics
We gratefully acknowledge the support of the Australian Research Council.