GENica
 Bioinformatics for Molecular Plant Breeding

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Sandbox

Welcome to the Genica Sandbox! This page is for editing experiments. Feel free to try your skills at formatting here. To edit, click edit this page at the top of the page, make your changes in the dialog box, and click the Save page button when you are finished. Content added here will not stay permanently; this page is automatically cleaned every 12 hours.


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Contents

MPBCRC-compatible colours

OFFICIAL MPBCRC ICON COLOUR AS PER DESIGNER BRIEF: PMS 362 = R:51 G:158 B:53 = #339e35  
MPBCRC COLOUR 02 (from .ppt slide template): #8cb531  
MPBCRC COLOUR 03 (from .ppt slide template): #decebd  
MPBCRC COLOUR 03 "light" (not from .ppt slide template): #f2ece6  
MPBCRC COLOUR 04 (from .ppt slide template): #218429  
MPBCRC COLOUR 05 (from .ppt slide template): #c6ce63  
MPBCRC COLOUR 05 "light" (not from .ppt slide template): #f8f9eb  


MPBCRC COLOUR 06 (from .ppt slide template): #b2b2b2  
MPBCRC COLOUR 06 "light" (not from .ppt slide template): #e2e2e2  


Workshop

Workshop

Systems Biology
From Single Cells to Environments
Melbourne 15-26 May


Workshop

Workshop

Systems Biology
From Single Cells to Environments
Melbourne 15-26 May


Workshop

Workshop

Systems Biology
From Single Cells to Environments
Melbourne 15-26 May

Bioinformatics Tools and Resources in GENica

The current Bioinformatics Tools and Resources in GENica are listed here in groups and can be accessed via the navigation tool bar on the left hand side of this page. Help


Markers and Mapping  
CMap cereal & legume Can be used to align maps and search for syntenies
Marker Binner An application for placing molecular markers into "bins" (also referred to as "panels" or "kits") according to their product sizes. (Password required)

cow


Comparative Genomic Analysis  
Cereal Blast
LegumeDB Blast
Son of Eric

Beer


Pedigree  
CERES Pedigree Prototype A prototype pedigree database for searching, viewing and editing pedigrees (Password required). Developed jointly by MPBCRC and the Department of Agriculture, Western Australia.

Pipet


Utilities  
MultidotterDotplots similarities for three or more DNA sequences. Requires input in FASTA format.
EMBOSSSuite of bioinformatic tools
Genbank sequence retrievalBatch retrieval, requires list of gi or accession numbers as input. Output can be in FASTA or in Genbank format.

Barley

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Some formatting experiments

  1. this
  2. is
  3. a list with an image cow
Could the wiki formatting be any more fun?

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Alt + 175 gives: » Also check out the Wikipedia Entry on Alt Keycodes...

To save a file, select File»Save As. Enter the name of the ... Go to MARKERS»SEARCH.

Italics

Sig --Ahunter 12:23, 24 Jun 2005 (WST)

More...

GEMMTOOLS MENU OPTIONS
MARKERS GEMDB FILES OPTIONS ADMIN
»SEARCH »SEARCH »LIST »EDIT MY DETAILS
»BIN MARKERS »ADVANCED SEARCH »UPLOAD »MY GROUPS

style="border-top:1px solid red; border-right:1px

         solid red; border-bottom:2px solid red; border-left:1px solid red;" 


Click on a 'GENica MARKER TOOLS' menu item below for explanations on its function
MARKERS
»SEARCH
»BIN MARKERS
»MARKER SETS
»IMPORT
»EXPORT
GEMDB
»SEARCH
»ADVANCED SEARCH
»PROJECT
»IMPORT
FILES
»LIST
»UPLOAD
OPTIONS ADMIN
»EDIT MY DETAILS
»MY GROUPS


Click on a 'GENica MARKER TOOLS' menu item below for explanations on its function
MARKERS
»SEARCH
»BIN MARKERS
»MARKER SETS
»IMPORT
»EXPORT
GEMDB
»SEARCH
»ADVANCED SEARCH
»PROJECT
»IMPORT
FILES
»LIST
»UPLOAD
OPTIONS ADMIN
»EDIT MY DETAILS
»MY GROUPS


Click on a 'GENica MARKER TOOLS' menu item below for explanations on its function
MARKERS
»SEARCH
»BIN MARKERS
»MARKER SETS
»IMPORT
»EXPORT
GEMDB
»SEARCH
»ADVANCED SEARCH
»PROJECT
»IMPORT
FILES
»LIST
»UPLOAD
OPTIONS ADMIN
»EDIT MY DETAILS
»MY GROUPS

Log in to GENica Marker Tools

Find information on other 'GENica Marker Tools' menu options

Click on a 'GENica MARKER TOOLS' menu item below for explanations on its function
MARKERS
»SEARCH
»BIN MARKERS
»MARKER SETS
»IMPORT
»EXPORT
GEMDB
»SEARCH
»ADVANCED SEARCH
»PROJECT
»IMPORT
FILES
»LIST
»UPLOAD
OPTIONS ADMIN
»EDIT MY DETAILS (non admin)
»MY GROUPS (non admin)
»MARKER DB IMPORT (group admin)
»USERS (group admin)
»GROUPS (group admin)

Log in to GENica Marker Tools

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Heading Level 2

Heading Level 3

Heading Level 4

Heading Level 5
Heading Level 6 "Lowest level"

Template:GENica Marker Tools user manual menu

Template: GMT Login

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NOTE: Markers can only be added to mrtmarker or binner marker sets. If you do not have access to a a marker set of either of these types, you can create a binner marker set by using the MARKER SETS ADD option.


Template:Brown box 95 percent

Template:Brown box 95 percent

*NOTE: The fields Run Name and Panel are not exported when using the GeneMapper® "Microsatellite Default" table settings. Entries for these fields can be entered through the GEMDB»IMPORT interface, see "How to use this option", step 6, on this page.
*NOTE: The fields Run Name and Panel are not exported when using the GeneMapper® "Microsatellite Default" table settings. Entries for these fields can be entered through the GEMDB»IMPORT interface, see "How to use this option", step 6, on this page.


UPDATES FOR THE MANUAL MENU TEMPLATE

Click on a 'GENica MARKER TOOLS' menu item below for explanations on its function.
MARKERS
»SEARCH
»SETS
»TAGS
»ADD
»IMPORT
»EXPORT
BINNER
»TAGS
»UPLOAD
GEMDB
»SEARCH
»ADVANCED SEARCH
»TAGS
»BROWSE
»IMPORT
FILES
»LIST
»UPLOAD
OPTIONS ADMIN
»EDIT MY DETAILS (non admin)
»MY GROUPS (non admin)
»MARKER DB IMPORT (group admin)
»USERS (group admin)
»GROUPS (group admin)
Click on a 'GENica MARKER TOOLS' menu item below for explanations on its function.
MARKERS OPTIONS: »SEARCH »SETS »TAGS »ADD »IMPORT »EXPORT
BINNER
GEMDB OPTIONS: »SEARCH »ADVANCED SEARCH »PROJECT »IMPORT
FILES OPTIONS: »LIST »UPLOAD
OPTIONS
ADMIN OPTIONS: »EDIT MY DETAILS (non admin) »MY GROUPS (non admin) »MARKER DB IMPORT (group admin) »USERS (group admin) »GROUPS (group admin)

The old GENica Welcome screen...

The bioinformatics tools and resources in GENica are listed here in groups and can also be accessed via the Bioinformatics Tools link at the top of this page.

Markers and Mapping

CMap cereal & legume

Marker Binner (Password required)
Comparative Genomic Analysis

Cereal Blast
LegumeDB Blast
Browse Son of Eric

Pedigree

A prototype pedigree database for searching and viewing breeding program pedigrees. Developed jointly by MPBCRC and the Department of Agriculture, Western Australia.

Pedigree prototype

Utilities

Multidotter dotplots multiple sequences
EMBOSS
Genbank sequence retrieval


GMT Tutorial Exercises for Automated Designers Overview


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