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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. A group may contain up to 10000 markers, so the program can be used to draw circular representations of genomic sequences.
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 Draws circular maps of DNA constructs Graph type [x11]: Input file [inputfile]: data.cirp do you want a ruler (Y or N) [Y]: type of blocks (enter Open, Filled, or Outline) [Filled]: 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 -ruler string do you want a ruler (Y or N) -blocktype string type of blocks: Open, Filled, or Outline. Option 'Outline' draws filled blocks surrounded by a black border -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 of 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) -textheight float height of text. Enter a number <1 or >1 to decrease or increase the size, respectively -textlength float length of text. Enter a number <1 or >1 to decrease or increase the size, respectively -tickheight float height of ticks. Enter a number <1 or >1 to decrease or increase the size, respectively -blockheight float height of blocks. Enter a number <1 or >1 to decrease or increase the size, respectively -rangeheight float height of range ends. Enter a number <1 or >1 to decrease or increase the size, respectively -gapgroup float space between groups. Enter a number <1 or >1 to decrease or increase the size, respectively -postext float space between text and ticks, blocks, and ranges. Enter a number <1 or >1 to decrease or increase the size, respectively Advanced qualifiers: (none) General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
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 |
-ruler | do you want a ruler (Y or N) | Any string is accepted | Y |
-blocktype | type of blocks: Open, Filled, or Outline. Option 'Outline' draws filled blocks surrounded by a black border | Any string is accepted | Filled |
-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) | Number from 0.000 to 360.000 | 90 |
-intersymbol | do you want horizontal junctions between blocks (Y or N) | Any string is accepted | Y |
-intercolor | color of junctions between blocks (enter a color number) | Integer from 0 to 15 | 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) | Integer 0 or more | 500 |
-ticklines | do you want vertical lines at the ruler's ticks (Y or N) | Any string is accepted | N |
-textheight | height of text. Enter a number <1 or >1 to decrease or increase the size, respectively | Any numeric value | 1 |
-textlength | length of text. Enter a number <1 or >1 to decrease or increase the size, respectively | Any numeric value | 1 |
-tickheight | height of ticks. Enter a number <1 or >1 to decrease or increase the size, respectively | Any numeric value | 1 |
-blockheight | height of blocks. Enter a number <1 or >1 to decrease or increase the size, respectively | Any numeric value | 1 |
-rangeheight | height of range ends. Enter a number <1 or >1 to decrease or increase the size, respectively | Any numeric value | 1 |
-gapgroup | space between groups. Enter a number <1 or >1 to decrease or increase the size, respectively | Any numeric value | 1 |
-postext | space between text and ticks, blocks, and ranges. Enter a number <1 or >1 to decrease or increase the size, respectively | Any numeric 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 20) 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 1000) 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, names will be written in the same color as the marker. Also, 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".
Program name | Description |
---|---|
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! |