OSfinder: A Tool for Accurate Orthology Mapping


To execute OSfinder, 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 genomic locations of anchors.
    "output-name"          -- output file prefix.
    "number-of-genomes"    -- the number of genomes under comparison.
    "minimum-segment-size" -- minimum length of orthologous segments.


Following options are available.

      -i  -- set file containing the genomic locations of anchors
      -o  -- set output name
      -n  -- set the number of genomes under comparison
      -s  -- set minimum length of orthologous segments (default=100000)
      -L  -- use "global maximization method" to optimize parameters
             (default is "local maximization method")
      -S  -- assume that input anchors are sorted
      -D  -- output detailed results
      -h  -- print help message

Sample Data

Our distribution includes following sample data file in the directory "samples/".

Execute OSfinder

To apply OSfinder on a sample data "mtu-mbo.murasaki.anchor.txt", type as follows.

% cd osfinder_v*_*/
% mkdir osfinder_results
% osfinder -i samples/mtu-mbo.murasaki.anchor.txt -o osfinder_results/mtu-mbo.murasaki -n 2 -s 10000

After the execution of OSfinder, three files will be created.

      -- file containing option values.

      -- file containing the genomic locations of the chains.

      -- file containing the genomic locations of the orthologous segments.

Compare eleven or more genomes

OSfinder can apply to orthology mapping among up to ten genomes. If you want to compare more genomes (e.g. 20 genomes) simultaneously, edit "src/osfinder.h" as follow.

      #define MAX_N 10  =>  #define MAX_N 20

Create input files for OSfinder

OSfinder requires an anchor file to be pre-computed. This page ("Make Input Files") explains how you can create the anchor files.

Visualize the output of OSfinder

The output of OSfinder includes the genomic locations of the chains and orthologous segments. Our distribution includes useful Perl scripts to visualize the results of OSfinder. This page ("Visualization") explains how you can visualize the results of OSfinder with our Perl scripts.

osfinder banner murasaki banner PHMMTS banner PSTAG banner