| Home | Download and Install | Getting Started | Make Anchor Files | Publications | Link |

OSfinder: A Tool for Accurate Orthology Mapping

Anchor File Format (Pairwise)

OSfinder assumes that anchor files have the form shown below when two genomes (G1 and G2) are compared.

      chrom_1 start_1 end_1 sign_1 chrom_2 start_2 end_2 sign_2

      chrom_1 -- chromosome ID on genome G1 (int).
      start_1 -- start coordinate on genome G1 (int).
      end_1   -- end coordinate on genome G1 (int).
      sign_1  -- orientation on genome G1 (char).
      chrom_2 -- chromosome ID on genome G2 (int).
      start_2 -- start coordinate on genome G2 (int).
      end_2   -- end coordinate on genome G2 (int).
      sign_2  -- orientation on genome G2 (char).

      Example)
      1 8040363 8040427 + 1 168782735 168782799 + 
      1 8847983 8848048 + 1 43731182  43731247  - 
      1 8849080 8849144 + 1 43730882  43730946  -
      1 8876198 8876273 + 1 108267190 108267265 +
    

Note that Chromosome IDs, start coordinates and end coordinates must be integer. Thus, "X" and "Y" are not appropriate for chromosome ID. In our experiment, we used "-1", "-2", "-3", and "-4" instead of "X", "Y", "2a", "2b", respectively.

Anchor File Format (Multiple)

OSfinder assumes that anchor files have the form shown below when three genomes are compared.

      20 55496602 55496695 + 10 31263560 31263653 + 1 16798400  16798493  +
      20 55496602 55496695 + 10 31263560 31263653 + 1 192688819 192688912 +
      20 55496602 55496695 + 10 31263560 31263653 + 1 228589428 228589521 +
      20 55496602 55496694 + 10 31263560 31263652 + 1 166624290 166624382 -