Genetic Map Drawer

Finding good free software to plasmids seems to be difficult. I have no idea why. When trying to draw a chromosomal map of pSymB from Sinorhizobium meliloti, I developed this little AWK script.

To begin, download the following script. On Linux, and MacOS, AWK is already available. On Windows, you can try GAWK for Windows; you'll have to, from the command line, type gawk drawmap.awk yourfile > outputfile. On Linux, MacOS, you can do a chmod a+x drawmap.awk just once, then ./drawmap.awk yourfile > outputfile.

DrawMap Script

You will have to describe the relevant features of your chromosome/plasmid in a plain text file. The first line, must be sizename where the size is in nucleotides. You can then describe all the regions in your chromosome. The following are recognized:

Feature	Syntax
Transposon on the outside	`t` name ntposition
Transposon on the inside	`T` name ntposition
Genes on the inside	`g` name ntposition
Genes on the outside	`G` name ntposition
Region defined by nucleotides	`r` name startnt stopnt ring
Region defined by transposons	`rt` name starttp stoptp ring
Highlighted sector/wedge by nucleotides	`s` startnt stopnt innerring outerring style
Highlighted sector/wedge by transposons	`st` starttp stoptp innerring outerring style
Highlighted sector/wedge by one transposon and one nucleotide position	`sT` starttp stopnt innerring outerring style

In the map generated, transposons were the features defining the regions, which were transposon-directed delitions; the name is somewhat misleading. The transposons are just features that have unique names between which you can define delitions. For example, here is a map for pSymB:

1683333 pRmeSU47b
t	Ω5079 26409
t	Ω5069 63194
t	Ω5085 106128
t	Ω5159 203182
t	Ω5143 290704
t	Ω5142 312356
t	Ω5146 347712
t	Ω5145 394879
t	Ω5140 428851
t	Ω5104 526421
t	Ω5133 541994
t	Ω5061 554255
t	Ω5102 590746
t	Ω5098 641546
t	Ω5047 735511
t	Ω5060 770089
t	Ω5045 820940
t	Ω5033 889262
t	Ω5026 914326
t	Ω5025 972983
t	Ω5020 979918
t	Ω5064 1044125
t	Ω5007 1084094
t	Ω5004 1108338
t	Ω5011 1177742
t	Ω5015 1259333
t	Ω5040 1298940
t	Ω5167 1371104
t	Ω5188 1413607
t	Ω5177 1452882
t	Ω5149 1489134
t	Ω5072 1543819
t	Ω5053 1563118
rt	ΔF117	Ω5060	Ω5033	1
rt	Δ5408	Ω5033	Ω5007	1
rt	Δ5416	Ω5007	Ω5011	1
rt	Δ5378	Ω5020	Ω5011	3
rt	ΔF114	Ω5033	Ω5007	2
rt	ΔG471	Ω5033	Ω5020	3
rt	ΔG470	Ω5020	Ω5007	4
rt	ΔG462	Ω5033	Ω5011	5
rt	ΔF514	Ω5047	Ω5061	1
rt	ΔF680	Ω5061	Ω5085	1
rt	ΔF693	Ω5142	Ω5085	2
rt	ΔF638	Ω5145	Ω5104	2
rt	ΔF909	Ω5047	Ω5085	3
rt	ΔF728	Ω5079	Ω5177	1
rt	ΔF726	Ω5079	Ω5149	2
rt	ΔG506	Ω5072	Ω5040	3
rt	ΔG373	Ω5079	Ω5177	4
rt	ΔK458	Ω5177	Ω5015	2
rt	∇1	Ω5069	Ω5085	6
rt	∇2	Ω5047	Ω5060	6
rt	∇3	Ω5015	Ω5011	6
g	dct	1626577
g	exo 1169222
g	lac 1
g	pca 1589460
g	thi 1633944
g	aga 1671025
g	bhb 1548979
g	dul 1255541

Lines starting with # are ignored. Also, you can highlight a wedge of the map using the s command. The formatting of the wedges is specified as an SVG style, with no spaces.

The default font is Iwona, which I quite like. If you edit the script, you can adjust the font easily in the BEGIN block, along with the radius of the plasmid, the various font sizes, the formatting of the ticks and region arcs and the formatting of the plasmid itself.