Message: 15Megblast GIs

Date: Sat, 7 May 2011 12:00:19 +0100

From: Peter Cock <p.j.a.cock@googlemail.com>

To: drhoads@uark.edu

Cc: galaxy-user@lists.bx.psu.edu, Galaxy Dev <galaxy-dev@bx.psu.edu>

Subject: Re: [galaxy-dev] [galaxy-user]

Message-ID: <BANLkTin6W-bh2H1KYPBQ0YinxTzVU32XJQ@mail.gmail.com>

Content-Type: text/plain; charset=ISO-8859-1

On Sat, May 7, 2011 at 12:01 AM, Douglas Rhoads <drhoads@uark.edu> 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).

Peter

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 should just have them reinstall the databases and make sure to use the correct switches?

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

drhoads(at)uark.edu, http://biscweb.uark.edu/drhoads

phone: 479-575-3251  FAX: 479-575-4010