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title: "Introduction"
canonical: "https://help.biobam.com/space/BCD/2250407980/Introduction"
format: markdown
---
**A Functional Annotation Pipeline:**  
The Blast2GO Command Line is a professional solution for integrating flexible, high-performance, and automated functional annotation tasks. It generates high-quality, reproducible results that seamlessly integrate into your data analysis workflows. The Blast2GO Command Line (CLI) version allows you to combine BLAST and InterPro XML results, map them against the Gene Ontology (GO) database, and assign the most suitable functional labels to uncharacterized sequence datasets.

With the command-line version, users can run GO analysis using a local database, which can be easily set up directly from the command line. Additionally, the CLI enables GO-Slim analysis and generates over 25 different summary charts along with a comprehensive PDF report for each analysis.

This version is based on the Blast2GO methodology, first published by [Conesa et al., 2005] for the functional annotation and analysis of gene or protein sequences. The method employs local sequence alignments (BLAST) to identify potential homologs for query sequences, ranging from one to hundreds of thousands. It then extracts all GO terms associated with these hits and returns an evaluated GO annotation for each query sequence. Enzyme codes are derived by mapping equivalent GOs, and InterPro motifs can be added directly to the BLAST-based annotation. A typical annotation process with Blast2GO involves four steps: BLAST and InterProScan, GO mapping, and functional annotation [Götz et al., 2008].

**Blast2GO CLI is designed for users who are already familiar with the Blast2GO methodology, such as those who have worked with Blast2GO or OmicsBox before, and are seeking:**

**High Performance:**  
The command-line version of Blast2GO allows you to analyze large datasets on your own computing resources, without needing a graphical user interface.

**Flexibility:**  
Integrate your functional annotation tasks into your custom analysis pipeline with ease, and run multiple analysis scenarios in parallel.

**Automatic Data Generation:**  
Automatically generate all statistical charts offered by Blast2GO. This includes a comprehensive PDF summary report, along with a wide range of images and text files.

**Reproducibility:**  
Control your entire analysis using a simple configuration file. This ensures you can easily set up different analysis strategies and reproduce scenarios for one or multiple datasets.

**Security:**  
Run BLAST and the Blast2GO annotation offline, on your own servers, according to your security requirements. Maintain full control over the data sources and versions used throughout the analysis.

## References

- Blast2GO: A Universal Tool for Annotation, Visualization and Analysis in Functional Genomics Research. Bioinformatics, 21(18):3674–3676.  - Conesa, A., Götz, S., García-Gómez, J. M., Terol, J., Talón, M., and Robles, M. (2005).
- High-Throughput Functional Annotation and Data Mining with the Blast2GO Suite. Nucl. Acids Res., pages gkn176+ - Götz, S., Garcia-Gomez, J. M., Terol, J., Williams, T. D., Nagaraj, S. H., Nueda, M. J., Robles, M., Talon, M., Dopazo, J., and Conesa, A. (2008).