BNL's Cotton Genome Project is building genetic linkage maps using MapMaker.
The project wants store and display gmap location information for each
marker using ACEDB. We hope that perhaps someone else has already written
some software to do at least part of our task of extracting the data from
MapMaker output files and getting it into ACEDB via .ace files.
The specific way the project is using MapMaker is as follows:
1. For each chromosome/linkage group/chromosome arm map, find a set of
"Landmark Loci" with threshold LOD scores of at least 3.
a. Denote these as Main_Marker for the map in ACEDB.
b. Compute Position for each Locus from cumulative inter-marker distances
2. Use MapMaker's "pairwise" command to produce a table of distances and LOD
scores for each of the other markers with each of the framework markers for
that chromosome/linkage group/chromosome arm.
3. Use data from #3 to compute map locations for non-framework loci,
using distances from markers with maximum LOD scores and using some kind
of inverse of the LOD score for Error (horizontal gmap placement) in ACEDB.
If anyone knows of software that already does something like this,
please send me email. Even if you don't know of anything that creates
.ace files, perhaps you might suggest where we might inquire to see
whether someone has done something to simply extract map positions
and errors from MapMaker output.
I'll be glad to post my findings, if any, back to the newsgroup.
Thanks,
-John
+=====================================================================+
| John L. McCarthy. . | Internet:..JLMcCarthy at lbl.gov |
| Computer Science R&D MS 50B-3238 | Bitnet: ...JLMCCARTHY at LBL |
| Lawrence Berkeley Laboratory .| telephone: (510) 486-5307 |
| 1 Cyclotron Road . | |
| BERKELEY, CA 94720-9000, U.S.A. | FAX: (510) 486-4004 |
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