Blast2go: b2g4pipe

Blast2go is the gene ontology annotation program for eukaryotes.

Some time after 2012, it became commercialised, although the free usage of early version is still permitted.

Blast2go the program is GUI, but there is a command-line alternative called b2g4pipe.

The best version of b2g4pipe to use is

http://www.blast2go.com/data/blast2go/b2g4pipe_v2.5.zip

As this is the one Peter Cock uses for the Galaxy wrapper version 8 in March 2015.

Installation and configuration

Aspects required:

• blast2go.properties file
• databases

blast2go.properties

This is the main configuration file. A normal user can also have a copy in his/her directory , and can try and use it instead. Example:

Dbacces.dbname=b2g_nov11
Dbacces.dbhost=publicdb.blast2go.com

or

Dbacces.dbname=b2g
Dbacces.dbhost=localhost

databases

These are what is required:

• http://archive.geneontology.org/latest-lite/go_20160130-assocdb-data.gz (234M) (this is actually a mysql dump)
• ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz(236M)
• ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2accession.gz (578M)
• ftp://ftp.pir.georgetown.edu/databases/idmapping/idmapping.tb.gz (2900M)