Help information for this website

Graphical interface
We have four main graphical representations of the maize genome results.
  • Plot regions of similarity of one chromosome with the rest of the genome
  • Plot colliear runs between a pair of chromosomes
  • Plot results from different maps or methods side-by-side
  • Plot an individual collinear run in detail
With the exception of the last plot, these images are all clickable to find more details. The user can specify the significance threshold of runs to plot, and also set limits (minimum and maximum) on the number of map elements included in a collinear run.
MySQL tables
The results available on this website are from four different maize genetic maps. For each map dataset we have a link to the marker map data we used in our analyses, and the results under different implementations of the LineUp software (FullPermutation, or FastRun, with different D values).

Detailed results lists every marker pair for every collinear run identified. The table has the format:
  • c1 reference chromosome
  • c2 compared chromosome
  • marker marker name
  • c1_pos position of the marker on c1
  • c2_pos position of the marker on c2
  • block_id id number for the collinear run (block)
  • id unique id number for every pair listing


Results overview lists summary information for each collinear run. There is only one line for each run.
  • c1 reference chromosome
  • c2 compared chromosome
  • len number of pairs involved in the collinear run
  • sum_square sum of square statistic used for significance calculations
  • c1_s start position of the run on c1
  • c1_e end position of the run on c1
  • c2_s start position of the run on c2
  • c2_e end position of the run on c2
  • sig significance level of the collinear run
  • block_id id number for the collinear run (block). This matches with the block_id in the Detailed Results table
  • id another unique id number for every listing
Installation and running of the software (readme file)
To uncompress and expand the file enter the following on the (UNIX) command line 
tar xzvf lineup.tgz
This includes the files:
LineUp/lineup.c
LineUp/lineup2mysql.pl
LineUp/lineup2txt.pl
LineUp/lineup.pl
LineUp/lineup_input.pl
LineUp/install.pl
LineUp/README
LineUp/pio99_marker_map
The pio_marker_map is a sample dataset, and was used in our analysis.
To install the LineUp program, first change directory into the lineup directory, and then enter 
perl ./install.pl
Any 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. 
lineup.c: In function `read_data':
lineup.c:271: warning: unknown escape sequence `\)'
lineup.c:279: warning: unknown escape sequence `\)'
lineup.c:290: 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 lineup_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 
./lineup.pl
This 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.mysql
replacing the databasename and basename.mysql as appropriate.
If you opt to have plain text output, there will be two output files
  1. basename_overview.txt - summary information for each run found
  2. basename_detail.txt - details of the individual markers in each run