BLast2GO config for local WWWBlast server. What am I doing wrong?

[beeman]

Hi, I have a local www-blast server running that I'm trying to query through Blast2GO to speed up some annotation. I've followed a couple of guides that are provided online, but I believe there may be a misconfiguration in the blast2go.properties file that is perhaps creating a problem and would apreciate some input from anyone who has achieved this before.

I've provided a screenshot with all the relevant information that shows the configuration and that the blast server is accepting blastx queries.

When configuring Blast2GO (by editing blast2go.properties), I edited 2 fields only.
- the Blast.urls field to include the url of my www-blast server
- the Blast.dbs field to include the database & server with a single space between these entries ("nr http://myserver.address/blast/blast.cgi").
Then after opening the blast dialogue in Blast2GO, I noticed the blast2go.properties file had been modified to include the Blast.blastdb field referencing the nr data base I want to query on our local server. This was automatically added by the program.

As you can see from the screengrab, I'm getting the error "Problem sending data to the NCBI BLAST Server. For input string "". Check Blast Mode: blastX, blastP, etc"

Can anyone suggest how to troubleshoot or resolve this? I'm stumped.

EDIT: I should say, if I blast against the NCBI server, it works fine, suggesting this is a config error with pointing to the local blast server.

Thanks.


EDIT: image removed

[GenoMax]

Since you are using a local blast server do you need the NCBI blast URL's in the config file?

BTW: You should modify firewall settings to appropriately restrict access. Your blast server is accessible from the internet (you probably don't want that).

[beeman]

Unfortunately the config file gets modified by the program to include the ncbi url each time it's run and editing the config file while it's already running doesn't seem to make any difference.

Thanks for the heads up re access.

[GenoMax]

Have you tried omitting the "nr http://cpebrazor.ivec.org/blast/blast.cgi" from Blast.blastdbs? Since it appears that you want to use the nr database that is local (and the name is the same as the NCBI database) you may not need that line.

Quote from the Blast2GO help below (highlighted part is a bit vague and does not mention the need to add a URL):

If your specific database is NOT at this server, but somewhere else, then you have to provide at the blast.properties file the url of the blast server, adding this at the Blast.urls line, and also the name of the database at the Blast.blastdbs. When you open B2G, you can select then the new blast server url and the blast db. You also have to change then Blast Mode to WWW-Blast at the Blast2GO Blast Configuration Menu.

[beeman]

Ok fixed. The main problem was I had to select www-blast in the blast options instead of qblast and this was not possible without activating the program with a trial key.

[GenoMax]

So your configuration as captured in the screenshot was correct?