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EMBOSS: cirdna |
It uses the graphical shapes: ticks, ranges, and blocks to represent genetic markers (e.g, genes and ESTs) and places them according to their position in a DNA fragment. The markers can be organized in different groups.
The program reads in one input file in which the user specifies the names and positions of the genetic markers. In this file the user also enters data for controlling the appearance of the markers.
A refined customization of the drawing can be achieved by running the program with '-options' on the command line and changing the values of the desired parameters.
% cirdna Graph type [x11]: Input file [inputfile]: data.cirp ticks inside or outside the circle (enter In or Out) [Out]: text inside or outside the blocks (enter In or Out) [In]:
Mandatory qualifiers:
-graphout graph Graph type
-inputfile infile input file containing mapping data
-posticks string ticks inside or outside the circle (enter In
or Out)
-posblocks string text inside or outside the blocks (enter In
or Out)
Optional qualifiers:
-originangle float position of the molecule's origin on the
circle (enter a number in the range 0 - 360)
-intersymbol string do you want horizontal junctions between
blocks (Y or N)
-intercolor integer color for junctions between blocks (enter a
color number)
-interticks string do you want horizontal junctions between
ticks (Y or N)
-gapsize integer interval between ticks in the ruler (enter
an integer)
-ticklines string do you want vertical lines at the ruler's
ticks (Y or N)
-tickheight float height of ticks (enter a number to multiply
the default height)
-blockheight float height of blocks (enter a number to multiply
the default height)
-rangeheight float height of range ends (enter a number to
multiply the default height)
-gapgroup float space between groups (enter a number to
multiply the default space)
-postext float space between text and ticks, blocks, and
ranges (enter a number to multiply the
default space)
Advanced qualifiers: (none)
General qualifiers:
-help bool report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
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| Mandatory qualifiers | Allowed values | Default | |
|---|---|---|---|
| -graphout | Graph type | EMBOSS has a list of known devices, including postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows, x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm, png | EMBOSS_GRAPHICS value, or x11 |
| -inputfile | input file containing mapping data | Input file | inputfile |
| -posticks | ticks inside or outside the circle (enter In or Out) | Any string is accepted | Out |
| -posblocks | text inside or outside the blocks (enter In or Out) | Any string is accepted | In |
| Optional qualifiers | Allowed values | Default | |
| -originangle | position of the molecule's origin on the circle (enter a number in the range 0 - 360) | Any integer value | 90 |
| -intersymbol | do you want horizontal junctions between blocks (Y or N) | Any string is accepted | Y |
| -intercolor | color for junctions between blocks (enter a color number) | Any integer value | 1 |
| -interticks | do you want horizontal junctions between ticks (Y or N) | Any string is accepted | N |
| -gapsize | interval between ticks in the ruler (enter an integer) | Any integer value | 500 |
| -ticklines | do you want vertical lines at the ruler's ticks (Y or N) | Any string is accepted | N |
| -tickheight | height of ticks (enter a number to multiply the default height) | Any integer value | 1 |
| -blockheight | height of blocks (enter a number to multiply the default height) | Any integer value | 1 |
| -rangeheight | height of range ends (enter a number to multiply the default height) | Any integer value | 1 |
| -gapgroup | space between groups (enter a number to multiply the default space) | Any integer value | 1 |
| -postext | space between text and ticks, blocks, and ranges (enter a number to multiply the default space) | Any integer value | 1 |
| Advanced qualifiers | Allowed values | Default | |
| (none) | |||
---------------------------------------------------------------------- Start 1001 End 4270 group label Block 1011 1362 3 ex1 endlabel label Tick 1610 8 EcoR1 endlabel label Block 1647 1815 1 endlabel label Tick 2459 8 BamH1 endlabel label Block 4139 4258 3 ex2 endlabel endgroup group label Range 2541 2812 [ ] 5 Alu endlabel label Range 3322 3497 > < 5 MER13 endlabel endgroup -------------------------------------------------------------------------
Blank lines in the input file are ignored.
The file is organized in several fields separated by one or more space or TAB characters.
The first non-blank line gives the start position of the DNA fragment to be drawn after the keyword 'Start'. The end position is on the second line following the keyword 'End'.
Then, one or more groups (up to a maximum of 100) of genetic markers are defined. Each group begins with a line consisting of the keyword 'group' and ends with a line consisting of the keyword 'endgroup'.
If desired, a group name can be given on the very next line but will not be displayed (only for compatibilty with lindna).
Next, the individual markers (up to a maximum of 100) of the group are described. Each marker begins with a line consisting of the keyword 'label' and ends with a line consisting of the keyword 'endlabel'.
Do not start a new marker (by using a 'label' line) before you have closed the previous marker (by using an 'endlabel' line). You must end a previous marker specification before starting a new one. i.e. do not overlap marker specifications in the input file.
For each marker, the line following the 'label' line describes the marker. Three types of markers can be drawn: ticks, blocks, and ranges.
For a tick, the descriptive line begins with the keyword 'Tick', followed by the position of the tick in the DNA fragment, and a number from 0 to 15 specifying the color in which the tick will be drawn (a list of available colors is given below). If desired, a name can be written above the tick. This name must be given on the next line. If more than one name are given (one name per line), only the first one will be displayed.
For a block, the descriptive line begins with the keyword 'Block', followed by the start and end positions of the block in the DNA fragment, and the number of the block's color. If desired, a name can be written above or inside the block. This name must be given on the next line. If more than one name are given (one name per line), only the first one will be displayed.
For a range, the descriptive line begins with the keyword 'Range', followed by the start and end positions of the range in the DNA fragment. Next on the line are the types of boundaries that are to be drawn. The user can choose among '>', '<', '[', and ']' for both start and end boundaries. If none of these types is wanted for a given boundary, then a point '.' must be entered. Next is the color number. If desired, a name can be written above the range. This name must be given on the next line. If more than one name are given (one name per line), only the first one will be displayed.
For any type of markers, try to avoid long names.
The colors defined in the PLPLOT graphics library are:
0 "BLACK", 1 "RED", 2 "YELLOW", 3 "GREEN", 4 "AQUAMARINE", 5 "PINK", 6 "WHEAT", 7 "GREY", 8 "BROWN", 9 "BLUE", 10 "BLUEVIOLET", 11 "CYAN", 12 "TURQUOISE", 13 "MAGENTA", 14 "SALMON", and 15 "WHITE".
This format can also be used for the program "lindna".
| abiview | Reads ABI file and display the trace |
| lindna | Draws linear maps of DNA constructs |
| pepnet | Displays proteins as a helical net |
| pepwheel | Shows protein sequences as helices |
| prettyplot | Displays aligned sequences, with colouring and boxing |
| prettyseq | Output sequence with translated ranges |
| remap | Display a sequence with restriction cut sites, translation etc |
| seealso | Finds programs sharing group names |
| showalign | Displays a multiple sequence alignment |
| showdb | Displays information on the currently available databases |
| showfeat | Show features of a sequence |
| showseq | Display a sequence with features, translation etc |
| textsearch | Search sequence documentation text. SRS and Entrez are faster! |