Galaxy |

Note. Blast2GO may take a substantial amount of time, especially if running against the public server in Spain. For large input datasets it is advisable to allow overnight processing, or consider subdividing.

What it does

This runs b2g4Pipe v2.5, which is the command line (no GUI) version of Blast2GO designed for use in pipelines.

It takes as input BLAST XML results against a protein database, typically the NCBI non-redundant (NR) database. This tool will accept concatenated BLAST XML files (although they are technically invalid XML), which is very useful if you have sub-divided your protein FASTA files and run BLAST on them in batches.

The BLAST matches are used to assign Gene Ontology (GO) annotation terms to each query sequence.

The output from this tool is a tabular file containing three columns, with the order taken from query order in the original BLAST XML file:

Column	Description
1	ID of query sequence
2	GO term
3	GO description

Note that if no GO terms are assigned to a sequence (e.g. if it had no BLAST matches), then it will not be present in the output file.

This tabular file is called an "Annotation File" in the Blast2GO GUI. If you download the tabular file, and rename it to use the extension ".annot", then it can be opened with the Blast2GO GUI via the "File", "Load Annotation (.annot)" menu (keyboard shortcut ALT+L). You can then run some of the interactive analyses offered in the GUI tool.

Advanced Settings

Blast2GO has a properties setting file which includes which database server to connect to (e.g. the public server in Valencia, Spain, or a local server), as well as more advanced options such as thresholds and evidence code weights. To change these settings, your Galaxy administrator must create a new properties file, and add it to the drop down menu above.

References

If you use this Galaxy tool in work leading to a scientific publication please cite the following papers:

Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013). Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology. PeerJ 1:e167 https://doi.org/10.7717/peerj.167

S. Götz et al. (2008). High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res. 36(10):3420–3435. https://doi.org/10.1093/nar/gkn176

A. Conesa and S. Götz (2008). Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics. International Journal of Plant Genomics. 619832. https://doi.org/10.1155/2008/619832

A. Conesa et al. (2005). Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674-3676. https://doi.org/10.1093/bioinformatics/bti610