GMT Tutorial Exercise 9

Search GEMDB - Find lines where recombination between parental alleles has occurred

This kind of search can be useful e.g. in marker-assisted selection approaches. The example below demonstrates how recombinants with specific alleles at two loci can be identified. However, there is no limit to the number of loci that can be searched for user-specified allele values at the same time, by building more and more complex searches.

1. Select GEMDB and then select SEARCH.
2. Find the allele scores for the parental lines. In the example dataset, all the parents' names begin with "P" (P1, P2, P3, P4):
   1. Select Tag: All
   2. Select Group: All
   3. Select Project: "your name_demo" (created in Exercise 4, and where demo genotype data was imported in Exercise 5. Please ensure both exercises have been completed beforehand.)
   4. Select Run: "2005-11-28_Plate1"
   5. Select Other filters for searching: 'Sample Name' and enter 'P%' as the keyword for which to search this field. GMT recognises wildcards '%' and '_'. "%" is used for any number of characters (including none), "_" is used for exactly one character.
   6. Leave all the "following" settings (Marker, Allele, Range "¦) at their defaults or blank.
   7. Click Search
   8. View Results for this search. In the tutorial example, this finds allele scores for all the parental lines. In the next step, you will search the example data set for lines where recombination between marker hv0149 and marker hv0215 has occurred.
3. Select all samples that have an allele score of 186 for marker hv0149, as parent 4 (P4).
   1. Leave Tag, Group, Project and Run at their previously entered settings.
   2. Do not select any of the fields available under Other. Do not enter a search string.
   3. Select Marker: "hv0149"
   4. Select Allele: Any
   5. Select Range: Enter '186' in the first text box.
   6. Ensure that only the Original Values box is ticked.
   7. Click Search, take note of the search number in the Search History table, e.g. "2".
4. Select all samples that have an allele score of 150 for marker hv0215, as parent 2 (P2).
   1. Leave Tag, Group, Project and Run at their previously entered settings.
   2. Do not select any of the fields available under Other. Do not enter a search string.
   3. Select Marker: "hv0215"
   4. Select Allele: Any
   5. Select Range: Enter '150' in the first text box.
   6. Ensure that only the Original Values box is ticked.
   7. Click Search, take note of the search number in the Search History table, e.g. "3"
5. Search all the samples that have both an allele score of 186 for marker hv0149 and of 150 for marker hv0215 (recombinants)
   1. In the Combine Searches text box, enter the search numbers for the results obtained in steps 3 and 4 above, separated by AND (e.g. "2 AND 3").
   2. Click View Results. Only samples that fill both the search conditions for the two combined searches are displayed.
   3. Try the different display options, and download the search results, if desired.
6. Tag the combined search results for future retrieval:
   1. Click Tag all results.
   2. In the tagging interface that opens, enter a Name for the new tag and choose GEMDB tag from the drop-down box.
   3. This opens the TAGS»GEMDB interface. Next to the new tag, click on View Markers. Alternatively, the tagged results can from now on be selected with the Tag drop-down box in GEMDB»SEARCH.

• Tip: You can build up your searches to become more complex, please also refer to the GMT online help pages to read more about the difference between the "OR" and "AND" operator and about the use of brackets to define operator precedence.