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Start Blast2GO by Java Web Start

IMPORTANT NOTE: (PLEASE read the WHOLE page. It will save us time!)


The minimum requirement to run Blast2GO is a working Java installation (version > 1.5) (on Win,Linux,Mac etc.) In case you do not have that already please install the actual Java Runtime Environment (JRE) from

By Java Web Start technology (which is included in JAVA) you will be provided with the latest Blast2GO update each time you start the application. If your browser hasn't been set up to run Java WebStart JNLP files, the link above will download a file called blast2go_cipf.jnlp. Some browsers will ask you what you want to do with the JNLP file (instead of automatically downloading it somewhere, or presenting it to you as text). If a dialog appears with “Open using application…” on it, use the javaws application to run your file (and check the box marked “Don't ask me again”):

  • <path to java runtime installation>/bin/javaws
  • <path to jdk installation>/jre/bin/javaws
  • javaws.exe

Download Blast2GO

Please select the amount of your system memory (RAM) to improve the performace of Blast2GO:

Please select:
256 MB 512 MB 1000 MB 1500 MB 1800 MB 2000 MB 3000 MB
very small projects default > 10000 seqs > 15000 seqs > 20000 seqs > 25000 seqs and 64 bit CPU > 40000 seqs and 64 bit CPU

Blast2GO needs more memory? → Use the dynamic memory JNLP URL:<put here the amount of memory you need>

Blast2GO Database Issues

To connect to the B2G database you (your computer settings, your personal firewall) and your institute (institutes firewall, providers network settings) has to permit outgoing tcp connections on port 3306. Normally outgoing connections of this type are always permitted unless you have a highly restrictive network policy. (To easily test if B2G works fine press one of the green arrows in the B2G main frame, some GO graphs should appear more or less instantly.

  • The current DB is called b2g_jun11, older one: b2g_may10
  • The database server IP is:
  • Older DBs: b2g_may10 at

Other Blast2GO database servers with the possibility to request access

Location Institution Version (Month/Year) Contact E-Mail
Indiana, USA Purdue University 09/2009 Rick Westerman westerman(at)purdue(dot)edu

B2G says “Thank You!” for the collaboration!
If you also want to contribute and make your database accessible to other researchers close to you please contact us.

Trouble Shooting

In case you have had troubles running Blast2GO due to some incompatibilities with any older versions of Blast2GO installed on your system or problems during some update process: Please remove the installed Blast2GO versions by Java Web Start AND delete manually the blast2go directory in your user account. In this way Blast2GO can install the correct version when starting the next time.
A list of possible BLAST databases you can access with BlastGO here.

Useful hints for Linux users

  • On 64 bit Linux machines javaws is not available from Sun for the 64 bit bit jre package, so you need to install the 32 bit jre application as well.
  • check Java: “java -version”
  • check/find Java Web Start: “whereis javaws”
  • Run Java Web Start: “javaws -viewer” (in the Java Control Panel, under “Advanced”, set console to “show console”)
  • Start B2G from command line: “javaws
  • Try the database connection from a Linux console with: “mysql -h193.144.127.204 -ublast2go -pblast4it b2g_jun09”
  • Set the right java version using “alternatives”:
    • bash$> sudo update-alternatives –install ”/usr/bin/javaws” “javaws” ”/usr/lib/jvm/java-6-sun-” 1
    • bash$> sudo update-alternatives –set javaws /usr/lib/jvm/java-6-sun-
start_blast2go.txt · Last modified: 2011/09/06 14:01 by sgoetz
Bioinformatics and Genomics Department
Centro de Investigación Príncipe Felipe
Valencia, SPAIN
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