General musings from the MacVector team about sequence analysis, molecular biology, the Mac in general and of course your favorite sequence analysis app for the Mac!

Using Blast and Entrez in MacVector with a proxy server

Blast and Entrez connect to the NCBI server using the normal “http” ports (exactly the same as if it was a web browser). If a web browser can access the NCBI’s server then MacVector should be able to.

The address for the Blast server is:

http://www.ncbi.nlm.nih.gov:80/blast/Blast.cgi

However, if you get the following error message then it’s possible that a proxy server is installed on your network and will need to be configured within MacVector.

Screenshot 08 02 2013 12 27

MacVector does not honour the system wide proxy settings that are configured in the System Preferences of OS X. This is due to the NCBI toolkit that MacVector uses to access Entrez and Blast. The only way that this can be configured in MacVector is to place the configuration for the proxy server settings in the following file:

~/Library/Preferences/ncbi.cnf

(That’s the Library folder in the user’s HOME directory and not the system Library folder).

The configuration is as follows where “PROXY SERVER HOSTNAME is the hostname or IP address of the proxy server.

[CONN]
HTTP_PROXY_HOST=
HTTP_PROXY_PORT=3128

Incidentally the Library folder is hidden by default in Lion and Mountain Lion. To view this hold down the OPTION key and then click on the GO menu in Finder.

You will need to be running MacVector 12.6 or higher for this to work.

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