File Menu

Main Menu Items


Description

Recent files

Allows reopening recently closed projects.

Open file

Open an OmicsBox project (.b2g/.box).

Save and Save as

Save the current project.

Close Tab

Close the selected tab.

Load

Allows loading ID and ID-Value lists into OmicsBox.

Export

Allows exporting the desired information to some file types, such as text or GFF.

Manage License

Check the license you currently have and change the activation key.

Preferences

Set the OmicsBox configuration.

Data Import and Export

Under the File menu and the Tools sub-menu, there are several useful features that can be used to manipulate sequence data.

Load

  1. Extract and import sequences from a FASTA and a GFF/GTF file (figure 1). For further information, please link here.

  2. Load Blast and InterProScan results.

  3. Load ID lists.

  4. Load GTF/GFF2/GFF3

  5. Load Accession List: Load Gene Ontology annotations via an Accession list. 

  6. Load GeneSymbol List: Load Gene Ontology annotations via a GeneSymbol list.

  7. Load GI-List: load Gene Ontology annotations via a GenInfo Identifier (gi) list. Please consider the identifier to be between vertical bar e.g. gi|356569257|.

  8. Load Data from BioMart: Load Gene Ontology annotations from BioMart. For further details on how to load annotations, link here.

  9. Load EggNOG, Metagenomics and PfamScan annotations.

  10. Load metagenomic Kraken data.

  11. Load Count Tables and Differential Expression results.

  12. Load BAM and VCF files.

The Accession List and the GeneSymbol file should contain two columns (separated by tabs) per line. The first column the accession id or gene symbol and the second column may contain the corresponding taxonomy. The second column is optional.

Figure 1: Extract and import sequences from a FASTA and a GFF/GTF file.

Export Menu

The icon of each menu item indicates which object type is suitable for this menu item. 


Description

Export Table

Export the current Main Sequence Table for the selected sequences.

Generic Export

This option allows you to export all the desired information to a text file.

Export as Fasta

Export sequences of this project in fasta format.

Export as GFF

Export the annotations of this project as GFF file.

Export Blast Top-Hits

It will export the best-blast-hit for each sequence, this is the hit with the lowest e-value.

Export Mapping Results

Allows to export all the information obtained and used during the Gene Ontology mapping process as GFF formatted text file.

Export Annotations (.annot)


Export Annotation Descriptions


Export Annotations in GO Annotation File Format (GAF v.2)


Export GO Propagation

Exports the GO parents up to the root for the annotated sequences.

Export Sequences per GO (Gene Sets)


Export Metagenomics GO Annotations


Export Kraken Data

Export the Kraken data as text file.

Export GFF

This option is only visible if a GFF file is loaded in OmicsBox or if a GFF has been generated from Gene Finding. It is also possible to export a GFF with GO terms. For further details, link here.

Export KEGG Data

KEGG related information as tab separated text file.

OmicsBox File Export Menu

Figure 2: OmicsBox File Export Menu