Welcome to Blast2GO CLI - The functional analysis pipeline for command-line users.


A Functional Annotation Pipeline: The Blast2GO Command Line is a professional solution to integrate flexible, high-performance, and automatic functional annotation tasks.  Generate high-quality results in a reproducible way directly integrated into your data analysis workflows. The Blast2GO Command Line (CLI) version allows combining BLAST and InterPro XML results, to perform the mapping against the GO (Gene Ontology) database and to assign the most suitable functional labels to the un-characterized sequence dataset. The command line allows running the GO analysis with a local database that can be easily set up from the command line. Additionally, the CLI allows performing GO-Slim and to generate over 25 different summary charts and a comprehensive PDF report of each analysis. This command-line version is based on the Blast2GO methodology, first published in 2005, [Conesa et al., 2005] for the functional annotation and analysis of gene or protein sequences. The method uses local sequence alignments (BLAST) to find similar sequences (potential homologs) for one up to hundreds of thousands of query sequences. The program extracts all GO terms associated with each of the obtained hits and returns an evaluated GO annotation for all query sequences. Enzyme codes are obtained by mapping to equivalent GOs and InterPro motifs can directly be added to the BLAST-based annotation. A basic annotation process with Blast2GO consists of 4 steps: blasting and InterProScan, GO mapping, and functional annotation [Götz et al., 2008].

Blast2GO CLI is thought for users that are familiar with the Blast2GO methodology, i.e. have worked with Blast2GO or OmicsBox in the past, and are looking for:

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

  • Flexible
    Easily integrate your functional annotation tasks within your custom analysis pipeline and run different analysis scenarios in parallel.

  • Automatic Data Generation
    Generate all the statistics charts Blast2GO offers, in an automatic fashion. This includes a PDF summary report, as well as a wide range of images and text files.

  • Reproducibility
    Control the whole analysis with a simple configuration file. This allows you to set up different analysis strategies anpad to reproduce multiple scenarios for one or various datasets.

  • Secure
    Run BLAST and the Blast2GO annotation offline, on your own servers, according to your security requirements. Take 100% control of data sources and versions you use throughout the analysis


[Conesa et al., 2005] Conesa, A., Götz, S., García-Gómez, J. M., Terol, J., Talón, M., and Robles, M. (2005). Blast2go: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21(18):3674–3676.

[Götz et al., 2008] 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). Highthroughput functional annotation and data mining with the blast2go suite. Nucl. Acids Res., pages gkn176+