transcript of email 01-07-2014d0932

2014-08-29

use MAST to query translated pubmed est database
4 messages
Kurt Whittemore <kurtwhittemore@gmail.com> 	Fri, Jan 3, 2014 at 3:31 PM
To: meme@nbcr.net
Hi Meme Suite representative,

I would like to use MAST with some motifs from GLAM2 to query the pubmed est nucleotide database translated into protein.  How can I go about accomplishing this goal?  Thanks for any help and information you have to offer me!

Best regards,
Kurt Whittemore

Graduate Student
Arizona State University
BIODESIGN INSTITUTE
Center for Innovations in Medicine
1001 S McALLISTER AVE
TEMPE, AZ 85287
Charles Grant <cegrant@uw.edu> 	Sat, Jan 4, 2014 at 12:09 PM
To: Kurt Whittemore <kurtwhittemore@gmail.com>
Cc: meme@nbcr.net
Hi Kurt,

On Jan 3, 2014, at 2:31 PM, Kurt Whittemore wrote:

> I would like to use MAST with some motifs from GLAM2 to query the pubmed est nucleotide database translated into protein.  How can I go about accomplishing this goal?  Thanks for any help and information you have to offer me!
>

The current version of GLAM2 will create a MEME text format motif file as part of it's output. It will be named 'glam2.meme'. This file can be used as the motif input to MAST.

We don't included the Pubmed EST database among the databases on the MAST public web site. Also, the MAST public web application doesn't support the '-dna' option for MAST that translates nucleotide sequences into amino acids. This means that you'll have to download your own copy of the EST database as a FASTA file, and install your own copy of the MEME Suite command line tools.

The MEME Suite source can be downloaded here:

http://meme.nbcr.net/meme/meme-download.html

The documentation for the command line version of MAST will be included in the download and is available online here:

http://meme.nbcr.net/meme/doc/mast.html

In particular the '-dna' option will translate nucleotide sequences into amino acids. When this option is used the input motifs must be protein motifs.

Let us know if you have further questions.

Charles
Charles Grant <cegrant@uw.edu> 	Sat, Jan 4, 2014 at 12:14 PM
To: Kurt Whittemore <kurtwhittemore@gmail.com>
Cc: meme@nbcr.net
Hi Kurt,

On Jan 4, 2014, at 11:09 AM, Charles Grant wrote:

> Also, the MAST public web application doesn't support the '-dna' option for MAST that translates nucleotide sequences into amino acids. This means that you'll have to download your own copy of the EST database as a FASTA file, and install your own copy of the MEME Suite command line tools.

Whoops! Sorry, I forgot that the public MAST web application does support the '-dna' option. It's in the list of 'Optional' settings on the web page, the check box with the title: 'Search nucleotide database with protein motifs'.

You still have the problem that the EST database is not in our list of supported databases. If the database is less than 1Mb you can upload it to the public web application, but if it's larger than that, you'll still have to run a local copy of MAST to do the analysis.

My apologies for the confusion.

Charles
Kurt Whittemore <kurtwhittemore@gmail.com> 	Sat, Jan 4, 2014 at 2:19 PM
To: Charles Grant <cegrant@uw.edu>
Cc: meme@nbcr.net
Hi Charles,

Great thanks for all of the informative answers!

Best,
Kurt
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