European Molecular Biology Computing Network - Biocomputing Tutorials cri-map" Mapping

Typical CRIMAP build run

 

In this short, conceptual example, the CRIMAP build option adds loci D and E to an existing map of three loci, "A  B  C". The steps are as follows:
  1. choose the most informative locus of the two, D,
  2. evaluate the four possible placements of locus D in the existing map, 
    D  A  B  C
A  D  B  C
A  B  D  C
A  B  C  D
    first using data from phase known meioses,
  3. discard any of these four possible maps having a likelihood score more than PK_LIKE_TOL worse than the most likely map, thus retaining 
    D  A  B  C
A  D  B  C
  4. see that this number of possible maps is less than the maximum number tolerable, PK_NUM_ORD_TOL, and retain them all for testing with the next locus,
  5. choose the next most informative locus, E,
  6. evaluate the ten possible placements of locus E in the two existing maps, 
    E  D  A  B  C
D  E  A  B  C
D  A  E  B  C
D  A  B  E  C
D  A  B  C  E

E  A  D  B  C
A  E  D  B  C
A  D  E  B  C
A  D  B  E  C
A  D  B  C  E
    using phase known data,
  7. discard any of these ten possible maps having a likelihood score more than PK_LIKE_TOL worse than the most likely map, thus retaining only the first three of the second set of five, 
    E  A  D  B  C
A  E  D  B  C
A  D  E  B  C
  8. see that there are no more loci to add,
  9. extract from these three maps a set of "uniquely ordered loci", "A D B C",
  10. evaluate the five possible placements of locus E in this map, now using phase unknown data,
  11. discard any of these five possible maps having a likelihood score more than PUK_LIKE_TOL worse than the most likely map, thus retaining only the first two, 
    E  A  D  B  C
A  E  D  B  C
  12. see that there are no more loci to add,
  13. extract from these two maps the set of "uniquely ordered loci", "A D B C", and finally
  14. report this map with interlocus distances, and report the two possible positions of locus E, together with the likelihood of each.