The Blast2GO (B2G) Pipeline Version (B2G4Pipe) runs B2G without any
graphical interface. B2G is an GO annotation and functional analysis
systems based on sequence similarity (Blast). The program extracts GO
terms to each obtained blast hit by mapping to existent annotation
associations. An annotation rule finally assigns GO terms to the query
sequence. Additionally you can add domian/motif based GO term obtained
through InterProScan searches. If you provide a folder with these xml
files the application will parse the XML belonging to for each
sequence and adds/merges the deduced GO terms to the BLAST based
annotations, allways taking into account the GO Ture Path Rule.  By
the B2G Desktop Application (www.blast2go.org) annotation and
functional analysis can be visualized in graph form reconstructing the
GO relationships and colour-highlighting the most relevant areas.

The output files generated by B2G4Pipe are equivalent to the file
generated by the desktop application. The annotation file (.annot) is
a tab separated file containing the sequence names and gene ontology
IDs.  An additional row holds a sequence description. The B2G Project
File (.dat) is a proprietary format and can be opened with the B2G
desktop application to perform manual re-annotations or GO base
analysis (Graph-Visualization, Fisher 2X2, statistic, bar/pies
charts). The ".dat" generation is not recomended when working with
very large datasets due to memory limitations.