We have four main graphical representations of the maize genome results.
The results available on this website are from pio99 genetic maps. We have a link to the marker map data we used in our analyses, and the results under different implementations of the CloseUp software.
Detailed results lists every marker pair for every collinear run identified. The table has the format:
Results overview lists summary information for each collinear run. There is only one line for each run.
|Installation and running of the software (readme file)|
To uncompress and expand the file enter the following on the (UNIX) command line
tar xzvf closeup.tgz
This includes the files:
CloseUp/closeup.c CloseUp/closeup2mysql.pl CloseUp/closeup2txt.pl CloseUp/closeup.pl CloseUp/closeup_input.pl CloseUp/install.pl CloseUp/README CloseUp/pio99_marker_mapThe pio_marker_map is a sample dataset, and was used in our analysis.
To install the CloseUp program, first change directory into the closeup
directory, and then enter
perl ./install.plAny error messages will be written to the screen. The gcc compiler gives the following known error message, which do not affect the function of the program. If you see any other error messages, then there may be a problem.
closeup.c: In function `read_data': closeup.c:679: warning: unknown escape sequence `\)' closeup.c:687: warning: unknown escape sequence `\)' closeup.c:698: warning: unknown escape sequence `\)'The install.pl script will create the executable version of the C program, and will set some perl variables.
The input format is a text file with one line per marker name. A line starts
with the marker name followed by at least one space, and then the map
position(s) of the marker in brackets in the format
marker (pos chr, pos chr, pos chr) e.g.
php20554 (322 9) umc1465 (236.6 2) mmp20 (84.8 6) bnl6.32 (968 1) lim228 (947.2 1) rz444c (95.4 1, 102.6 6) umc1197(cat3) (675.4 4)If you already have your map data in a MySQL table you can use the closeup_input.pl script to create an input file from the MySQL table. You will probably need to edit this script so that the column names are correct for your table format.
The ONLY line you should edit is the following:
$st = "SELECT marker,chr,cM FROM $table";
replace 'marker' with the name of the column that holds the gene or marker name
replace 'chr' with the column that holds the chromosome information
replace 'cM' with the column that holds the map position information.
Please note that it does not matter if your data are bp positions, rank order positions, cM positions, or any other map unit.
To run the program enter
./closeup.plThis is a perl script which provides a more comfortable interface to the C program and the results parsers.
If you opt to have MySQL output, the results file will end .mysql, and you can send this into your mysql database with the command
mysql -p databasename < basename.mysqlreplacing the databasename and basename.mysql as appropriate.
If you opt to have plain text output, there will be two output files