GENica MARKER TOOLS Manual

About GENica Marker Tools

• 'GENica Marker Tools' is a place to store, search and edit GeneMapper^®-generated microsatellite marker data, Luminex^® FlexMAP^® microsphere-based SNP data and DArT^® marker data. It particularly serves the use of Multiplex-Ready^TM markers and gives access to tools that support the set-up and analysis of genotyping experiments with multiplex-ready markers.
• The application was created and is being further developed by the Centre for Comparative Genomics (CCG) for the Molecular Plant Breeding Cooperative Research Centre (MPBCRC).
• To receive a user account, please contact Gregory Lott.
• For questions, comments and suggestions, please contact Gregory Lott (User Support) or Adam Hunter (Technical Leader, software development).

How to use this manual

• Please click on the task description below to read the relevant help manual item. The manual provides detailed information on GENica Marker Tools features.
• To move between help manual sections, either follow the cross-links in the text, or the 'Links to other user manual pages' box, available on every page of the help manual. For every 'GENica Marker Tools' "main menu" item, there is a box with the corresponding "submenu items". To find out e.g. about the FILES»UPLOAD function, click on »UPLOAD underneath FILES.
• The help manual pages have the same names as the corresponding menu and submenu items in 'GENica Marker Tools'. The HELP links in 'GENica Marker Tools' will immediately open the relevant help page in a new window.
• For a "hands-on" introduction, including access to demo input files, work through the tutorial exercises instead.

The 'GENica Marker Tools' modes of function

MARKERS

• Search an online version of the Multiplex Ready Technology^TM marker database for information on curated marker sets for Barley and Wheat.
• Search for a marker's map position(s) in CMAP, an on-line comparative map viewer.
• Create and manage your own marker sets.

BINNER

• Bin MRT^TM markers, i.e. create marker panels for multiplex-ready^TM SSR markers without allele overlaps, that can be analysed together in a capillary sequencer.
  Use either default allele size information compiled for MRT^TM markers for wheat and barley, or import your custom marker information.
• Bin 'Single Nucleotide Polymophism' (SNP) markers, i.e. group SNPs that can be analysed together on the Luminex platform in FlexMAP microsphere-based oligonucleotide ligation assays (OLA) or allele-specific primer extension (ASPE) assays.

GEMDB

• Store, search and edit SSR data for your research projects (restricted to SSR data in GeneMapper® output format).
• Share data within a group or with all 'GENica Marker Tools' users.
• Correct allele size data for effects of dye drift and the extra length introduced by the MRT^TM tag (if applicable).
• Search for samples with specific genotypes, e.g. to identify recombinants.
• Search across a data set for replicates with conflicting allele values.

DARTS

• 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.
• The GENica Marker Tools "DARTS" module allows storing DArT^® genotype data in a relational database.
• Perform advanced searches across the "DARTS" module.

SNPDB

• The GENica Marker Tools "SNPDB" module allows storing SNP genotype data in a relational database.
• Perform advanced searches across the "SNPDB" module.

TAGS

• Tag markers to group them, e.g. as input for BINNER»MRT TAGS.
• Tag GEMDB entries to select markers to be binned.
• Tag GEMDB, SNPDB or DARTS entries for further work or to delete them from GEMDB, SNPDB or DARTS.
• Tag samples in GEMDB, SNPDB or DARTS for further work or to delete them from GEMDB, SNPDB or DARTS.

FILES

• Up-load files (restrictions apply) you want to share with other 'GENica Marker Tools' users.
• Download the most up-to-date version of the "Automated Designer" macros (Excel files), user manuals (PDF files) and data format templates from here.

OPTIONS

• Select your preferred display and export options.

ADMIN

Users without "group administrator" status:

• View details of the user groups you belong to.
• View and edit details of your user account.

Users with "group administrator" status:

• View and create user groups.
• View and create users.
• Add users and administrators to the groups they administer
• Import SSR marker information into a marker set belonging to one of your groups.
• Import SNP marker information into a marker set belonging to one of your groups.

Selected group admin users only:

• Import DART marker information into marker set "Triticarte DArT Makrers" belonging to user group "Triticarte". (This information is not yet available.)

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Links to other user manual pages

I'd rather try the tutorial...

• Get started with the GMT Tutorial
  Log in to 'GENica Marker Tools'