Introduction

Blast2GO is a comprehensive bioinformatics tool for the functional annotation and analysis of genome-scale sequence datasets. The software was originally developed to provide a user-friendly interface for Gene Ontology annotation. Over the last years, many improvements have considerably increased the functionality of Blast2GO and many different functional genomics tools are now available. Additionally, the application offers a wide array of graphical and analytical tools for data manipulation and mining. The main concept behind the developments is the easiness for biological researchers: minimal set up requirements, automatic updates, simplicity in the usage and visual-oriented information display. Advanced functionality is instantly available requiring a minimal computational background. Basically, Blast2GO uses local or remote BLAST searches to find similar sequences to one or several input sequences.

The program extracts the GO terms associated to each of the obtained hits and returns an evaluated GO annotation for the query sequence(s). Enzyme codes are obtained by mapping from equivalent GOs while InterPro motifs are directly queried at the InterProScan web service. GO annotation can be visualized reconstructing the structure of the Gene Ontology relationships  A typical basic use case of Blast2GO consists of 5 steps: BLASTing, mapping, annotation, statistical analysis and visualization. These steps will be described in this document including installation instructions, further explanations and information on additional functions.