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OSfinder: A Tool for Accurate Orthology Mapping

Usage

To run OSinfder, type as follows:

      % osfinder -i anchor-file -o output-name -n number-of-genomes [-s minimum-segment-size] [-L] [-S] [-D] [-h]
      
      "anchor-file"          -- file containing the coordinate spans for anchors.
      "output-name"          -- output file prefix.
      "number-of-genomes"    -- the number of genomes under comparison.
      "minimum-segment-size" -- minimum length of orthologous segments.
    

Options

Following options are available.

      -i  -- set file containing the coordinate spans for anchors
      -o  -- set output name
      -n  -- set the number of genomes under comparison
      -s  -- set minimum length of orthologous segments (default=100000)
      -L  -- set "global maximization method" as the parameter optimization method
             (default is "local maximization method")
      -S  -- assume that input anchors are sorted according to its start coordinate
      -D  -- output detailed results
      -h  -- print help message
    

Sample Data

Our distribution includes following sample data.

(1) "mtu-{mbo,mle,mpa}.murasaki.anchor.txt" -- pairwise anchors between M. tuberculosis (Mtu) and either of M. bovis (Mbo), M. leprae (Mle), or M. avium (Mpa). These anchors were detected by Murasaki (seed weight was set at 30 and seed length was set at 45).

(2) "mtu-mbo-{mle,mpa}.murasaki.anchor.txt" -- multiple anchors among M. tuberculosis (Mtu), M. bovis (Mbo), and either of M. leprae (Mle) or M. avium (Mpa). These anchors were detected by Murasaki (seed weight was set at 30 and seed length was set at 45).

(3) "mtu-{mbo,mle,mpa}.blastp.anchor.txt" -- pairwise anchors between M. tuberculosis (Mtu) and either of M. bovis (Mbo), M. leprae (Mle), or M. avium (Mpa). These anchors were detected by BLASTP program with E-value threhold 10e-100.

Execute OSfinder

To test OSfinder, type as follows:

      % cd osfinder_v1_0/
      % mkdir samples/your_results
      % osfinder -i samples/data/mtu-mbo.murasaki.anchor.txt -o samples/your_results/mtu-mbo.murasaki -n 2 -s 10000
    

After the execution of OSfinder, three files are created.

      "outputname.options"
      -- file containing option values.

      "outputname.chain.txt"
      -- file containing the coordinate spans for chains.

      "outputname.os.txt"
      -- file containing the coordinate spans for orthologous segments.
    

Draw Dot-Plot

Our distribution includes a script to draw dot-plots. The script can be applied to anchor files, chain files and orthologous segment files. An example of the command is as follows:

      % perl -w scripts/draw_dot_plot.pl -i samples/data/mtu-mbo.murasaki.anchor.txt -a 1 -b 1

      -i  -- set anchor (chain, or orthologous segment) file name.
      -a  -- chromosome ID of genome 1.
      -b  -- chromosome ID of genome 2.
      -o  -- set output file name.
    
When '-o' option is not used, output file name will be set as "anchor-file-name.png".

Compare eleven or more genomes

OSfinder can apply to orthology mapping among up to ten genomes. If uses want to compare more genomes (e.g. 20 genomes), edit "src/osfinder.h" as follow.
    #define MAX_N 10  =>  #define MAX_N 20