User Manual 1.4.4


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. The Command Line 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 Features

  • High-performance analysis of large datasets on your own computing resources without a graphical user interface.
    • Access to the high-performance CloudBlast and CloudInterProScan.

    • Gene Ontology mapping of Blast results with a local database.

  • Best-practice functional annotation

  • GO-Slim reduction 
  • Many statistics charts
  • Multiple data import and export options

System Requirements

  • Blast2GO Command-line tools are designed to work on all three major platforms (Linux, Mac OS, Windows).
  • Java 8
  • We recommend at least 2 GB of ram.
  • For a local Blast2GO database, a MongoDB server (version 3.4.6+) is needed.


Our support and development team works closely together to take care of all the trouble you might have. It does not matter if the issue is rather technical or about bioinformatics or biology. You can reach us at and we will do our best to answer all requests within one day. All comments and suggestions regarding our services are most welcome and a valuable source of information for us.