Functional Analysis
Blast2GO Annotation, (GOs, COG, Enzymes, Domains), Enrichment Analysis, Visual Exploration

Functional Analysis Module

The OmicsBox Functional Analysis module is a well-known comprehensive bioinformatics tool for the functional annotation.

High-Throughput Blast and InterProScan

Use CloudBlast and CloudInterProScan to perform fast sequence alignments and domain searches against reference datasets of your choice.

Gene Ontology Mapping

Link potential homologs and domains with available functional annotation from up-to-date well-curated databases from UniProt and Gene Ontology consortia.

Blast2GO Annotation

The Blast2GO methodology allows to flexibly assign most reliable functional labels to novel sequence datasets, taking into account source annotation quality and ontology hierarchies.

Enrichment Analysis

Use different enrichment analysis approaches (Fisher Exact Test and GSEA) to identify over and under represented molecular functions. 

Combined Pathway Analysis

Identify Reactome and KEGG pathways for any set of sequences, use differential expression data to calculate pathway enrichment (GSEA) and a combined visualization to gain insights with ease.

  • Blast in all variations
    • CloudBlast in high-performance cloud
    • Public NCBI databases
    • Local with own databases
  • GO Mapping
  • GO Annotation
  • GO-Slim
  • InterProScan
    • CloudIPS in high-performance cloud
    • Public EMBL service
  • EggNOG annotation in high-performance cloud
  • Enzyme commission number annotation
  • RFAM for coding potential
  • Statistics to evaluate every step
  • GO graphs to overview annotations
    • Combined graphs for whole datasets
    • Specific GOs
    • Colored GO graphs
  • Enrichment analysis
    • Fisher Exact Test
    • Gene Set Enrichment Analysis
  • Longest ORF prediction
  • Sorting and filtering of whole datasets
  • Versatile import and export possibilities in many formats

Blast2GO Methodology

The well known Blast2GO annotation methodology, first published in 2005, is now part of  OmicsBox. Blast2GO is the leading bioinformatics platform for the analysis of novel genomes, internationally recognized by the scientific community with over 7000+ research citations.

Everything in One Place

Load a FASTA file and analyze it step by step with the Blast2GO methodology to obtain high-quality functional annotations. All data in one place with full control over all analysis parameters.

KEGG Combined Pathway Analysis

This tool allows to identify pathways from multiple pathway databases for any set of sequences. In combination with differential expression data the tool allows to calculate pathway enrichment. A result table allows to filter for enriched pathways with linked, differentially expressed, genes.


Gene Set Enrichment Analysis

Convenient histograms and distribution charts help you to evaluate every stage in your analysis to get the most out of your data. 

Gene Ontology Graphs

Visualize the annotations as GO graphs to get a good overview. In continuation, filter and shape the graph to bring out and present your conclusions clearly and neat.


Whole Tomato Genome

Characterized Genes
high-quality annotated
1 %
processing time
1 h


Gene Ontology Annotation

This is the full Gene Ontology annotation workflow using cloud-powered algorithms (Blast, InterProScan, GO Mapping) to get the most complete annotation labels. Detailed statistics of every step are generated to summarize results. Combined graphs for the three categories (Biological Process, Molecular Function and Cellular Component) are generated including the annotations from InterProScan results. The final project contains all the data generated in every step.