GMT Tutorial Overview

• In this tutorial, users will be introduced to GENica Marker Tools (GMT) through a series of exercises covering its main functions.

• Please complete all the exercises listed under "General Functions" first. The exercises for "GEMDB", "DARTS" and "MRT^TM MARKERS" can be selected according to interest. Where an exercise requires completion of another exercise, this is indicated in the text.

• Please send your questions and comments regarding this tutorial and GENica Marker Tools to Gregory Lott.

General Functions

Exercise 1: Login to GENica Marker Tools
Exercise 2: Navigate across GENica Marker Tools
Exercise 3: Download tutorial materials from FILES
Exercise 4: Create a project for genotyping data storage

GEMDB

GEMDB is a database for storing, searching and editing GeneMapper^®-generated microsatellite marker data.
Exercise 5: Import a GeneMapper *.txt file into GEMDB
Exercise 6: Browse GEMDB
Exercise 7: Search GEMDB - Find the number of allele entries available for a specific marker in a project
Exercise 8: Search GEMDB "“ Retrieve all the data in a GEMDB project, but exclude data for specified markers
Exercise 9: Search GEMDB "“ Find lines where recombination between parental alleles has occurred
Exercise 10: Identify conflicting allele values in GEMDB
Exercise 11: Delete all the results for a marker from GEMDB

DARTS

DARTS is a database for storing, searching and editing DArT^® data. DArT^® (Diversity Arrays Technology) markers were developed by the people at Diversity Arrays Technology P/L; DArT^® genotyping services are offered to the wheat and barley community through their subsidiary, Triticarte P/L. Please refer to these companies' websites for information on the technology and on available services.
Exercise 12: Import data into DARTS
Exercise 13: Browse DARTS
Exercise 14: Search DARTS "“ Find markers with a marker quality score of 90.00 and above
Exercise 15: Search DARTS - Find the number of missing data for a marker
Exercise 16: Delete all the results for a marker from DARTS

MRT^TM MARKERS

GMT offers access to online and downloadable applications supporting the use of Multiplex-Ready^TM markers.
Exercise 17: Search the Multiplex-Ready^TM Marker database
Exercise 18: Bin multiplex-ready^TM markers
Exercise 19: Select an "Automated Designer" to automate your work with MRT^TM markers
Exercise 20: The Automated Designers - How to use the Polymorphism Viewers
Exercise 21: The Automated Designers "“ How to perform marker screening using the "Whole Genome Scan" marker kits
Exercise 22: The Automated Designers - How to perform marker screening using a custom set of markers
Exercise 23: The Automated Designers - How to use the genetic analysis macros

SNP MARKERS

GMT gives access to information on single nucleotide polymorphism (SNP) markers that were adapted by Matt Hayden to be analysed by "FlexMAP microsphere"-based ASPE assay on the Luminex platform. A "SNPBINNER" has been developed to support multiplexing of markers for this assay.
Exercise 24: Search the SNP markers database
Exercise 25: Bin SNP markers

SNPDB

SNPDB is a database for storing, searching and editing SNP data, e.g. as generated in "FlexMAP microsphere"-based OLA or ASPE assays on the Luminex platform.
Exercise 26: Converting "raw" Luminex data to genotypes with the SNPscorer macro
Exercise 27: Import data into SNPDB
Exercise 28: Browse SNPDB
Exercise 29: Search SNPDB - Find samples whose AR values fall outside the defined thresholds
Exercise 30: Delete records from SNPDB
Exercise 31: Change the "species" entry for samples in SNPDB