Main Menu Items
Allows reopening recently closed projects.
Open an OmicsBox project (.b2g/.box).
Save and Save as
Save the current project.
Close the selected tab.
Allows loading ID and ID-Value lists into OmicsBox.
Allows exporting the desired information to some file types, such as text or GFF.
Check the license you currently have and change the activation key.
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 Blast and InterProScan results.
Load ID lists.
Load Accession List: Load Gene Ontology annotations via an Accession list.
Load GeneSymbol List: Load Gene Ontology annotations via a GeneSymbol list.
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|.
Load Data from BioMart: Load Gene Ontology annotations from BioMart. For further details on how to load annotations, link here.
Load EggNOG, Metagenomics and PfamScan annotations.
Load metagenomic Kraken data.
Load Count Tables and Differential Expression results.
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.
The icon of each menu item indicates which object type is suitable for this menu item.
Export the current Main Sequence Table for the selected sequences.
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 KEGG Data
KEGG related information as tab separated text file.
Figure 2: OmicsBox File Export Menu