Latest revision as of 14:20, 8 February 2016

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:

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

These are what is required:

@@ Line 13: / Line 13: @@
 Aspects required:
- * blast2go.properties file
+* blast2go.properties file
- * databases
+* databases
 ==blast2go.properties==
@@ Line 21: / Line 21: @@
   Dbacces.dbhost=publicdb.blast2go.com
+or
+ Dbacces.dbname=b2g
+ Dbacces.dbhost=localhost
 ==databases ==
-These are what is required.
+These are what is required:
-El fichero '''blast2go.properties''' contiene los datos de las BBDD necesarios para '''Blast2go''' en las siguientes líneas:
-* http://archive.geneontology.org/latest-lite/go_20120526-assocdb-data.gz ('''105M'''), se trata de un '''dump''' SQL.
+* 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('''157M''')
+* ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz('''236M''')
-* ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2accession.gz ('''373M''')
+* ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2accession.gz ('''578M''')
-* ftp://ftp.pir.georgetown.edu/databases/idmapping/idmapping.tb.gz ('''900M''')
+* ftp://ftp.pir.georgetown.edu/databases/idmapping/idmapping.tb.gz ('''2900M''')
-En el caso de nodo '''chubby''', las bases de datos son locales (instaladas anteriormente) que hace que sea mucho más rápida el programa. Por tanto, la ubicación de las BBDD es:
- Dbacces.dbname=b2g
- Dbacces.dbhost=localhost