Local Blast2go database installation 2016

1. Note 1: Use the “silent mode” (-s) to produce less output and to speed up the import. (On a Windows system use also (-b) to suppress the beep when errors occur.)
   Note 2: You can alternatively also first open a mysql shell and than use the command “source” to import the data.

1. Import the next two files (yet unzipped) you downloaded from NCBI with:
   gene2accession

   mysql -h dbhost -u dbuser -p dbpass b2gdb -e "LOAD DATA LOCAL INFILE '/your/path/to/gene2accession' INTO TABLE gene2accession FIELDS TERMINATED BY '\t' LINES TERMINATED BY '\n';"

   mysql -h dbhost -u dbuser -p dbpass b2gdb -e "LOAD DATA LOCAL INFILE '/your/path/to/gene_info' INTO TABLE gene_info FIELDS TERMINATED BY '\t' LINES TERMINATED BY '\n';"

   Note: On a Windows system the ‘\t’ has to be replaced by a “\t”.

1. To import the mapping file obtained from PIR we will use the following command:

   java -cp .:mysql-connector-java-5.0.8-bin.jar: ImportIdMapping /your/path/to/idmapping.tb localhost b2gdb blast2go blast4it

   Note: On a Windows system, replace the java classpath separator “:” with “;”.
   This step can take several hours, please be patient.

Congratulations, you are done. To test your installation, check again the new database settings in Blast2GO and click on the green little arrows in the main application window. If the green GO graphs pop up you database is working correctly.