OmniMapFree - Design

Updated: 14 July 2011.

Introduction

It is very easy to customise OmniMapFree to display genome maps of your favourite organism.

Map Name

Change the name of the exe file e.g. changing OmniMapFree.exe to FgraMap.exe and FgraMap will appear in the title bar of the map window, also FgraMap will replace OmniMapFree in the Help/About OmniMapFree menu item and the About OmniMapFree dialog box.

Menus and Folders

The menu shown at the top of the map window mirrors the folders in the OmniMapFree directory on your hard disk - except the File, Search, Reset and Help menu items (there are no folders for these) and the Temp menu item and folder is always required (it is used by the Search function).

The File and Search menus always come first - at the left of the menu bar. The Reset and Help menus always come last. The other menus are arranged alphabetically.

There are some special folders: _data, _seqs and _stats. Any folder name beginning with an underscore "_" is not shown as a menu item. These folders have special functions, described later.

If a folder has sub-folders this creates menu items with sub-menus - see Proteins or Transcriptomics in FgraMap.

When OmniMapFree begins running it checks the folders and sub-folders in the same directory as the OmnniMap.exe file and uses them to create the menu system in the map window. If a folder is empty or begins with an underscore it is not included as a menu. The files within a folder become menu items within that menu. The menu items are arranged alphabetically - so if you want "Zgenes" to come before "Agenes" you have to rename these files/folders e.g. "1_Zgenes" and "2_Agenes" etc.

Also its best to avoid spaces in filenames e.g. rename "Gene clusters" to "Gene_clusters".

_data folder

This folder contains several text files containing basic information required by OmniMapFree to draw the genome including:

chromosomes

This essential file contains a list of the chromosomes and their length in base pairs. You will need to provide this for your organism. For each chromosome the data is on a separate line using the format "id=length" e.g. in FgraMap

1=11723881
2=8987179
3=7751167
4=8065741

where chromosome 1 has length 11,723,881 base pairs etc.

genes

This essential file contains a list of the genes found on each chromosome. You will need to provide this for your organism. This has the same format as a posn data file (see later) except that the annotation column is optional.

# clRed
# chrom	start	end	strand	name	annotation
1	1152	2202	+	fg11579	hypothetical protein
1	3147	3735	-	fg11580	hypothetical protein
1	6064	8172	+	fg11581	conserved hypothetical protein
1	8773	9129	+	fg11582	hypothetical protein
1	9682	13090	-	fg11583	hypothetical protein
1	13820	14151	+	fg11584	hypothetical protein
1	15153	16740	+	fg11585	probable cytochrome P450 55A2
1	18070	18798	-	fgd475-90	hypothetical protein
1	32344	32914	-	fgd486-10	hypothetical protein
1	33063	37418	-	fgd487-10	related to ankyrin
...
colours

This essential file contains a list of the extended colours recognized by OmniMapFree. This does not need to be changed. Each colour is on a separate line and has the format "colourname=$RGB". Each colourname has a "cl" prefix.

clAliceblue=$FFF8F0
clAntiquewhite=$D7EBFA
clAquamarine=$D4FF7F
clAzure=$FFFFF0
clBeige=$DCF5F5
clBisque=$C4E4FF
clBlanchedalmond=$CDEBFF
clBlueviolet=$E22B8A
clBrown=$2A2AA5
...
fasta files

These files are not essential but are useful. They are DNA fasta sequence files, one for each chromosome. OmniMapFree will work without them but will not be able to save sequences of selected regions of the map. If you provide them they should have names like "1.fasta" where "1" is the ID of the first chromosome as used in the chromosomes file.

>FG_Chromosome_1 # MIPS fg_chromosomes.tar.gz (2006.08.31)
GAAAGGCGTGCAAATGCGGATTCGCGACTTCCATCCGCAGCCATGTCCGCACGTTCCATAAGGAGCTGGCCCTTTCGAAA
AAGGAGCTCAAGAAGTACGAGGAATCCTTTAGGGACCTATCTCCCATCTGTGACCGCAATGTTATCCGGAATCTACAACC
CAGCTCGCAAGACCCAGTAATCCCTTACCTCCCCATTCATCTCGATAATATCCTATGCCTCAGCTATAAGGATCAGAAGC
GACTATATATATGCCATTCTAAAACGCATATATAAGAGCATTTCCGTCTTATCTATAGTTGAAAATCCCACTATTATAGC
...

_seqs folder

You do not need to put any files here. This folder is used by OmniMapFree for saving sequences of selected regions. They are named like "id_fragment.fasta" where id is the ID of the chromosome from which the fragment was extracted.

Remember to copy and rename these files if you want to keep them because they are overwritten by subsequent selected region saves!

_stats folder

You do not need to put any files here. This folder is used by OmniMapFree to save lists of genes on each chromosome (id.genes.txt) and for simple statistics of gene density on each chromosome (stats).

Next -> Data files