Question: blast2go local www-blast not working

[AdrianP]

Hello,

I posted this on BioStar and Blast2GO google group, so far nothing.
http://www.biostars.org/p/87104/#87109

https://groups.google.com/forum/#!topic/blast2go/id6FnS3wVuU

Problem:
I followed the tutorial and setup local nr and nt databases and was able to get them working on the web interface, and was able to link them to my blast2go, and select the local server as a www-blast database.

A problem I am encounter however, is that no matter what I blast, i get no results returned. When I blast manually on the web server, I get a result, when I feed it to blast2go, and start the blast, everything gets no results returned.

This is somewhat odd. I even tried asking for my server for an Blast XML response, when I used the web server to search, and that worked just fine.

There is not much to go on, since there is no error anywhere... I was wondering if you had encountered this before? blast on NCBI right now works horrible for me, sometimes 5-10 minute per query... so I need to get the local one working asap.

My properties file for blast2go show: Blast.url=http://137.122.148.173/blast/blast.cgi Blast.urls=http://www.ncbi.nlm.nih.gov/blast/Blast.cgi,http://137.122.148.173/blast/blast.cgi Blast.blastdb=nt

Thank you for your time. Adrian

P.S. The URL is not accessible externally, only for people on intranet, but blast is run from a machine that has access to intranet. Hopefully that doesn't screw things up, there are no proxies setup.

[westerman]

Well, step #8 of the B2Go "www-blast tutorial" says:

Add you [sic] database and the www-blast path to the B2G properties file (/home/your_user_name/blast2go/blast2go.properties) Blast.blastdbs=nr,swissprot,your_new_db Blast.urls=http://localhost/cgi-bin/blast/blast.cgi (seperated [sic] from others by a white space)

Note the latter -- separate your urls by white space. Not by comma as given in your properties file. Failing that I would just take out the NCBI blast server entirely. Why bother keeping it if it is too slow for you?

[AdrianP]

I tried making the changes, leaving my URL as the only one in both lists, however there is no change in the blast2go behavior, still says no results returned.

[westerman]

Well, I probably can't help much more. First I don't use B2Go very much these days. Second when I was using it extensively I always did the blasting outside of B2Go (it can be quicker that way) and then imported the file into B2Go. This can be impractical before some people though.

What happens if, instead of changing the properties file, you from the GUI window go to 'Data Access Configuration'. Can you get it working from that angle?

[eriklysoe]

Had the same problem with blast2go and managed to solve it removing link to ncbi (just had the local) and changing blastmode (or something, not on computer now) to www-blast. Then it worked. I can be more specific later when I see the blast2go property file

[rhinoceros]

Well, I probably can't help much more. First I don't use B2Go very much these days. Second when I was using it extensively I always did the blasting outside of B2Go (it can be quicker that way) and then imported the file into B2Go. This can be impractical before some people though.

I'd say it's way more practical than having to setup a blast server

[eriklysoe]

As mentioned here, local blast outside blast2go is faster. Not shure why

[eriklysoe]

Another thing, I managed to set up the local blast2go database, and the mapping and annotation is superfast. That is really time saving