lindna Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Draws linear maps of DNA constructs Description lindna draws linear maps of DNA constructs. 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. It reads an input file containing the names and positions of the genetic markers, and data for controlling the appearance of the markers (drawing commands). The output is a plot with with the linear DNA map. Usage Here is a sample session with lindna % lindna -graph cps Draws linear maps of DNA constructs Commands to the lindna drawing program file [inputfile]: data.linp Draw a ruler [Y]: Open : Open blocks Filled : Filled blocks Outline : Black border Type of blocks [Filled]: Created lindna.ps Go to the input files for this example Go to the output files for this example Command line arguments Draws linear maps of DNA constructs Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-infile] infile [inputfile] Commands to the lindna drawing program file -[no]ruler boolean [Y] Draw a ruler -blocktype menu [Filled] Type of blocks (Values: Open (Open blocks); Filled (Filled blocks); Outline (Black border)) -graphout graph [$EMBOSS_GRAPHICS value, or x11] Graph type (ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, pdf, svg) Additional (Optional) qualifiers: -maxgroups integer [20] Maximum number of groups (Integer 1 or more) -maxlabels integer [10000] Maximum number of labels (Integer 1 or more) -intersymbol selection [Straight] Type of junctions between blocks -intercolour integer [1] Colour of junctions between blocks (enter a colour number) (Integer from 0 to 15) -interticks boolean [N] Horizontal junctions between ticks -gapsize integer [0] A zero value allows the application to choose a gap size (Integer 0 or more) -ticklines boolean [N] Vertical lines at the ruler's ticks -textheight float [1.0] Height of text. Enter a number <1.0 or >1.0 to decrease or increase the size, respectively (Number 0.000 or more) -textlength float [1.0] Length of text. Enter a number <1.0 or >1.0 to decrease or increase the size, respectively (Number 0.000 or more) -margin float [1.0] Width of left margin. This is the region left to the groups where the names of the groups are displayed. Enter a number <1.0 or >1.0 to decrease or increase the size, respectively (Number 0.000 or more) -tickheight float [1.0] Height of ticks. Enter a number <1.0 or >1.0 to decrease or increase the size, respectively (Number 0.000 or more) -blockheight float [1] Height of blocks. Enter a number <1.0 or >1.0 to decrease or increase the size, respectively (Number 0.000 or more) -rangeheight float [1.0] Height of range ends. Enter a number <1.0 or >1.0 to decrease or increase the size, respectively (Number 0.000 or more) -gapgroup float [1.0] Space between groups. Enter a number <1.0 or >1.0 to decrease or increase the size, respectively (Number 0.000 or more) -postext float [1.0] Space between text and ticks, blocks, and ranges. Enter a number <1.0 or >1.0 to decrease or increase the size, respectively (Number 0.000 or more) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-graphout" associated qualifiers -gprompt boolean Graph prompting -gdesc string Graph description -gtitle string Graph title -gsubtitle string Graph subtitle -gxtitle string Graph x axis title -gytitle string Graph y axis title -goutfile string Output file for non interactive displays -gdirectory string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit Input file format Input files for usage example File: data.linp Start 1001 End 4270 group exons label Block 1011 1362 3 H ex1 endlabel label Tick 1610 8 H EcoR1 endlabel label Block 1647 1815 1 H endlabel label Tick 2459 8 H BamH1 endlabel label Block 4139 4258 3 H ex2 endlabel endgroup group repeat-regions label Range 2541 2812 [ ] 5 V Alu endlabel label Range 3322 3497 > < 5 V MER13 endlabel 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. Spaces and tabulations are allowed but only the first 20 characters of that name (including spaces) will be displayed. 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, one or more names can be written above the tick. In this case an optional letter H or V should be added to the line. H or V indicate whether the text will be horizontal or vertical, respectively. If no letter is specified, H is assumed by default. A list of one or more names can be given on the next lines with one name per line. 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, one or more names can be written above the block. Names are given on the following lines. An optional letter H or V can be added to the end of the descriptive line to specify the orientation of the name(s). 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, one or more names can be written above the range. Names are given on the following lines. An optional letter H or V can be added to the end of the descriptive line to specify the orientation of the name(s). 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 "cirdna". Output file format Output is to the specified graphics device. Output files for usage example Graphics File: lindna.ps [lindna results] Data files None. Notes Whether to draw a rule and the type of block-fill style must be specified. There are many other (optional) qualifiers to control the appearance of the plot which will be prompted for if the program is run with -options on the command line and. References None. Warnings None. Diagnostic Error Messages None. Exit status It always exits with a status of 0. Known bugs None. See also Program name Description abiview Display the trace in an ABI sequencer file cirdna Draws circular maps of DNA constructs iep Calculate the isoelectric point of proteins pepinfo Plot amino acid properties of a protein sequence in parallel pepnet Draw a helical net for a protein sequence pepwheel Draw a helical wheel diagram for a protein sequence plotorf Plot potential open reading frames in a nucleotide sequence prettyplot Draw a sequence alignment with pretty formatting prettyseq Write a nucleotide sequence and its translation to file remap Display restriction enzyme binding sites in a nucleotide sequence showfeat Display features of a sequence in pretty format showpep Displays protein sequences with features in pretty format sixpack Display a DNA sequence with 6-frame translation and ORFs Author(s) Nicolas Tourasse formerly at: Biotechnology Center of Oslo Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Written (2000) - Nicolas Tourasse Updated (2002) - Nicolas Tourasse Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None