Opening Projects in Genome Workbench

Introduction

Genome Workbench organizes data around the concept of "Project". A "Project" is a named container, grouping information related to a certain topic of study. Projects can contain references to known molecules, sequence information, annotations, alignments, phylogenetic trees, etc. Projects can be named, saved and later reopened. Projects can organize data into folders.

projects

This tutorial will take you through the steps necessary to understand how the Project entity works in Genome Workbench.

Step 1. Download Experiment File

Please download the GFF3 experiment file.

Step 2. Add molecules to project

Open molecules:

CM001064.1 CM001065.1 CM001066.1 CM001067.1 CM001068.1 CM001069.1 CM001070.1 CM001071.1 CM001072.1 CM001073.1 CM001074.1 CM001075.1

Open Molecules Dialog

The result should look similar to this:

Molecules Loaded into the project

You can open a Table view in order to sort, filter, and search through large projects containing many sequence molecules. This view may make it easier to find a sequence accession of interest. To open the Table view, right click on the project name to launch the context menu, and click on the option "Open Table View".

Open Table View

Step 3. Import GFF file

Open the GFF file with gene models.

Import the GFF file

Choose Next, Next, Add to an existing Project, Finish.

Step 4. Remap local ids to accesions

The GFF3 file is formulated to use local ids, instead of accessions - use remapping information to import with accession ids.

SL2.40ch01 CM001064.1 SL2.40ch02 CM001065.1 SL2.40ch03 CM001066.1 SL2.40ch04 CM001067.1 SL2.40ch05 CM001068.1 SL2.40ch06 CM001069.1 SL2.40ch07 CM001070.1 SL2.40ch08 CM001071.1 SL2.40ch09 CM001072.1 SL2.40ch10 CM001073.1 SL2.40ch11 CM001074.1 SL2.40ch12 CM001075.1

Remap GFF ids

Step 5. Open Graphical View

Now your project contains two sets: molecules and annotations. If you open a molecule with Graphical View you will see your annotations.

Two projects and Graphical Sequence View

Conclusion

Genome Workbench allows you to better structure your work with Projects. It is important to remember that IDs are resolved within the scope of a single Project. Related sequences and annotations should therefore be loaded into the same Project. This applies both to molecules with NCBI accessions and to local data (imported from FASTA as well as annotation files like GFF).

Current Version is 3.7.1 (released October 13, 2021)

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Last updated: 2021-07-19T20:53:50Z