DREME: What is the meaning of letters that are not DNA or RNA letters

[Malik Yousef]

Hi

1. I'm running dreme and getting motifs that consists from letters that are not DNA or RNA letters such as seq="TKTATTW"

How to read those letters?

2. How one can get the output of DREME as MEME in text mode?

Best

Malik

[CharlesEGrant]

Hi Malik

The IUPAC DNA and RNA alphabets contains ambiguity symbols as well as symbols for the nucleotides. See also the MEME Suite documentation on alphabets.

The dreme.txt file generated DREME is in MEME text format. There should be a link to this file in the results for your job. You can also download MEME format files for individual motifs from the DREME HTML page. Click on the right pointing arrow in the "Submit/Download" column, then choose the "Download Motif" tab and click on the download button.

Charles

[Malik Yousef]

Thanks for your reply...

I see only the file dreme.xml and not dreme.txt.

I need to have the same output of DREME as MEME in the same format...how to do that?

Malik

[Malik Yousef]

I need to say that i'm running the command line from Cygwin.

[CharlesEGrant]

If you are only getting the dreme.xml file that would indicate that DREME is crashing before it's finished. Are you seeing any error messages in the DREME output? Were there any error messages in the build or installation process? This sort of error is mostly commonly caused by a missing module.

[Malik Yousef]

Yes i saw and error messages.

[Malik Yousef]

Creating HTML file.

      0 [main] python2.7 6148 child_info_fork::abort: address space needed by 'cyg                                                                   z.dll' (0x300000) is already occupied

Traceback (most recent call last):

  File "/home/user/meme/bin/dreme", line 1899, in <module>

    if __name__ == '__main__': main()

  File "/home/user/meme/bin/dreme", line 1896, in main

    run_xml_transformations(outdir)

  File "/home/user/meme/bin/dreme", line 1450, in run_xml_transformations

    if (subprocess.call([_html_prog, xml, html]) != 0):

  File "/usr/lib/python2.7/subprocess.py", line 522, in call

    return Popen(*popenargs, **kwargs).wait()

  File "/usr/lib/python2.7/subprocess.py", line 710, in __init__

    errread, errwrite)

  File "/usr/lib/python2.7/subprocess.py", line 1231, in _execute_child

    self.pid = os.fork()

OSError: [Errno 11] Resource temporarily unavailable

[CharlesEGrant]

Hi Malik,

Either something is wrong with your Cygwin installation or something went wrong with your installation of MEME Suite. Are you using the 32-bit or 64-bit version of Cygwin? We recommend the 64-bit version and have not tested MEME Suite with the 32-bit version for a few years. If you are running the 64-bit version of Cygwin I'd recommend reconfiguring and re-building MEME Suite, taking careful note of any error messages. That is, I'd recommend re-running these steps:

./configure

make clean

make &> make.log

make test &>test.log

You should check the files config.log, make.log, and test.log for any error messages. If you do find error messages please forward us the files. That will help us troubleshoot the problem.

[Malik Yousef]

Hi Charles

I have replied in private as i need to send couple of files.

Best

Malik