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:jen@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

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