Functional Analysis

Functional Annotation and Analysis of any sequencing data.

Sequence Analysis

High-Throughput Blast and InterProScan 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 and well-curated databases from UniProt and the Gene Ontology consortia.

Blast2GO Annotation

The Blast2GO methodology allows assigning the most reliable functional labels to novel sequence datasets, combining different sources of annotations like protein domains, and orthology groups of basic sequence similarities, always taking into account annotation quality and gene ontology hierarchies.

Enrichment Analysis

Use different enrichment analysis approaches like Fisher Exact Test and GSEA to identify over and under-represented biological 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.

Complete Feature List

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

Functional Analysis Module

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

Feature	Description	Beneftis
Functional Annotation with the Blast2GO Methodology	Combine multiple tools like Blast, InterPro, or EggNOG to design and run custom, high-performance annotation strategies.	Use any type of genomics, proteomics, or transcriptomics datasets to generate high-quality functional labels from scratch and directly proceed with the functional interpretation of results.
Combined Pathway Analysis	Find statistically significant altered pathways for any type of sequence dataset and visualize multiple pathway databases in combination with expression values.	Identify altered pathways and immediately track down potentially relevant elements, even for datasets without previously available information.
Functional Enrichment Analysis	Perform different types of statistically sound enrichment analysis like Fisher’s exact test or GSEA with full control of your background annotations and the tests details (FDR, Two Tailed, etc.)	Easily gain insights into the biological significance of your data by identifying overrepresented functions taking into account the Gene Ontology hierarchy.

Gold Standard Blast2GO Functional Annotation Methodology

The well-known Blast2GO annotation methodology, first published in 2005, is now part of OmicsBox. Blast2GO is the leading bioinformatics platform for analyzing novel genomes, internationally recognized by the scientific community with over 2000+ research citations.

– Generate or improve functional labels using the reliable and comprehensive Blast2GO method.

– Customize annotation strategies to suit your specific research needs.

End-to-End Functional Analysis Workflow

Achieve deeper insights into your omics data with robust annotation, pathway analysis, enrichment testing, and versatile visualization options.

Dive in: Functional Analysis Module Highlights

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. More Content About Gene Set Enrichment Analysis to match the length of KEGG Combined Pathway Analysis.

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.

Why work with Functional Analysis Module?

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.

Dataset and ID Adjustment

OmicsBox data integrity and consistency capabilities ensure accurate downstream analysis. Our dataset and ID adjustment options empower users to match their annotations through a variety of selection, filtering, renaming, and ID-mapping options.

This functionality guarantees that your data remains precise and reliable, facilitating seamless and efficient analysis.

Many Rich Visualizations

OmicsBox offers various ways to inspect results for each analysis step, including different charts like Bar, Venn, Box, or Bubble plots.

Review each analysis step with comprehensive visual tools, enhancing understanding and communication of results.

Benchmark

Whole Tomato Genome

Details

Characterized Genes

high-quality annotated

1 %

processing time

1 h

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