Message: 15Megblast GIs
Date: Sat, 7 May 2011 12:00:19 +0100
From: Peter Cock <>
Cc:, Galaxy Dev <>
Subject: Re: [galaxy-dev] [galaxy-user] 
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1

On Sat, May 7, 2011 at 12:01 AM, Douglas Rhoads <> wrote:
> We have a local install of Galaxy and are using it for training grad and
> undergrad students (using the Windshield Splatter data).? We have a
> relatively new install and the Megablast seems to be doing something funny
> with the output in that column 2 which is supposed to be the GI of the
> database hit is now two numbers joined with an underline (see below).? I
> need to tell my IT people what is wrong so they can correct the problem.
> BL1-1-3?????157649053_111750?????91.30????????46?????????????4??????????????0??????????????10?????????????55?????????????58541???????58496???????2e-
> 06?????????????60.0
> BL1-1-5?????161788633_175843?????100.00???????26?????????????0??????????????0??????????????15?????????????40?????????????48812???????48787???????4e-
> 04?????????????52.0

Which version of BLAST do you have?

If you're using the "megablast" tool in Galaxy, then it will be NCBI
"legacy" BLAST using the blastall binary.

If you're using the (commented out by default) BLAST+ wrappers, then
it will be using the blastn binary. There were changes to the ID
handling in the tabular output in BLAST 2.2.25+ as I recall.

Another important factor is how the BLAST database was made (with or
without the -parse_seqids flag).


P.S. Questions like this about local installs might be better on the
galaxy-dev list, CC'd.
Thanks Peter,  I debated which to post to.
This is just using the Megablast tool in Galaxy.  My IT people are not 
Biologists.  They had 
this working fine and some tweak has screwed up the GI column in the results 
file.  It should 
be the same NR and HTGS datafiles that we had before.  So you recommend that I 
just have them reinstall the databases and make sure to use the correct 

Douglas Rhoads,  Professor of Biological Sciences
Director of Graduate Program in Cell and Molecular Biology
601 SCEN, Dept. of Biological Sciences,
1 University of Arkansas, Fayetteville, AR 72701
phone: 479-575-3251  FAX: 479-575-4010
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