GMT Tutorial Exercise 24

Search the SNP markers database

SNP marker information is found in MARKERS»SEARCH, i.e. in the same GENica Marker Tools mode of function where MRT^TM marker information is stored, see also exercise 17.

1. Select MARKERS and then select SEARCH.
2. Select a Marker Set with SNP markers, e.g.:
   1. SNP MARKERS
      • "SNP Markers (MPBCRC:public:mhayden)" to search all SNP markers adapted by Matt Hayden to be analysed by "FlexMAP microsphere"-based ASPE assay on the Luminex platform.
   2. SNPDB tags
      • Choosing one of the tags created in SNPDB (e.g. in Exercise 30 or Exercise 31) allows viewing general marker info on tagged GEMDB markers.
3. To see all the available markers in a Marker Set, type the wildcard character '%' in the Search text box (immediately next to the Search button).
4. Click Search.
5. Try the different display options, in particular the 'SNP View' that was specially created for SNP marker info.
6. Try sorting the results table by different fields by clicking on different column headers.
7. Try filtering the results table with the different available options (Type, Prefix, Quality, etc.)
8. Try changing the fields displayed in the 'Custom view'. Do this in the Marker Custom Fields tab, available in the OPTIONS mode of function.
9. Try the CMAP link next to a marker of interest to search the MPBCRC CMAP Live installation for maps where a particular marker has been located.
10. Try to download data for a marker selection you are interested in.

• Tip: Refer to the GMT online help on the MARKERS»SEARCH interface for detailed information on the MRT markers database and on fields displayed in the different "Views".

The MARKERS»SEARCH interface, showing marker information for SNP markers in the SNP Markers (MPBCRC:public:mhayden) marker set, displayed in "SNP View". Note that only some of the fields in that view are visible in this screenshot.