Hello,
"nt" refers to the "nucleotide" database. It is also linked from the
link below, to here:
http://www.ncbi.nlm.nih.gov/nuccore
The "Quick start guide" can answer many questions about it:
http://www.ncbi.nlm.nih.gov/books/NBK44863/
A good technical content description is here:
ftp://ftp.ncbi.nlm.nih.gov/blast/db/README
For viral only, there is a genbank division "VRL", that could be used in
a local or cloud install with megablast:
http://www.ncbi.nlm.nih.gov/genbank/htgs/divisions/
There are other options, a quick search brings up many alternatives, but
you can review these to see which are the best fit for your own
project's goals.
Best,
Jen
Galaxy team
On 5/24/13 2:57 PM, Sun, Wenping [USA] wrote:
Jen,
Thank you very much for the information. They are very informative.
I found the htgs and wgs databases information there. What does nt
28-Jan-2013 stand for?
Meantime, if I am looking for virus containing database, I found wgs
is one. Can anyone confirm or advice further if there is other options
(database)?
Thank you again!
Kathryn
*From:*Jennifer Jackson [mailto:j...@bx.psu.edu]
*Sent:* Friday, May 24, 2013 3:36 PM
*To:* Sun, Wenping [USA]
*Cc:* galaxy-user@lists.bx.psu.edu
*Subject:* [External] Re: [galaxy-user] Question on megablast databases
Hi Kathryn,
These first three are three different types of sequence databases
available from GenBank The last is a genome assembly for the phiX174
genome.
Information about all can be found here:
http://www.ncbi.nlm.nih.gov/genbank/
There are many uses, one example is covered in our Metagenomics
publication:
https://main.g2.bx.psu.edu/u/aun1/p/windshield-splatter
Thanks!
Jen
Galaxy team
On 5/24/13 6:59 AM, Sun, Wenping [USA] wrote:
Dear galaxy members,
I have a question on the databases used in megablast module from
galaxy. There are four db options to blast against with -
1.htgs 28-Jan-2013
2.nt 28-Jan-2013
3.wgs 28-Jan-2013
4.phiX174
Is there any further information to guide which database would be
appropriate to use? In addition, how to find the genome
information contained in each database?
Many thanks,
Kathryn
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
