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MEME Suite Q&A

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Welcome to the MEME Suite question and answer forum.

As of Sept. 24 2025 the MEME Suite site is down due to a major system failure. We don't have an estimate of how long it will take to fix, but it may be a couple of weeks. We will post further information as it becomes available.

The latest version of the MEME Suite can be used online at http://meme-suite.org/.

You might get a more immediate response by sending an email to the support address meme-suite@uw.edu as more people from the team check that address and some of them even work on weekends...

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Sep 25

MEME Suite is down

The MEME Suite web site is down due to a major system failure. We don't have a reliable estimate

unread,

MEME Suite is down

The MEME Suite web site is down due to a major system failure. We don't have a reliable estimate

Sep 25

Sep 25

MEME Suite: inaccessible

Is the MEME-Suite down for all, or is it just me, or has it been discontinued like so many other

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MEME Suite: inaccessible

Is the MEME-Suite down for all, or is it just me, or has it been discontinued like so many other

Sep 25

Pipistrellus, cegrant2

Aug 28

MEME suite docker image install problem

That's not so much an error message as an informational message. We don't include the

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MEME suite docker image install problem

That's not so much an error message as an informational message. We don't include the

Aug 28

Xuan Wang, cegrant2

Aug 14

Could not access MEME

Our server was down due to a cooling system failure. It is running again now. On Wednesday, August 13

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Could not access MEME

Our server was down due to a cooling system failure. It is running again now. On Wednesday, August 13

Aug 14

Elaine wu, cegrant2

Jul 31

MEME analysis system didn‘t work for some unknown reason

The MEME Suite server was unable to submit jobs that day due to a network issue. It is now operating

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MEME analysis system didn‘t work for some unknown reason

The MEME Suite server was unable to submit jobs that day due to a network issue. It is now operating

Jul 31

XIYIN SHI, cegrant2

Jul 31

Full sequence output from AME

I'm not quite sure what you are looking for here, or if AME is the appropriate tool. The primary

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Full sequence output from AME

I'm not quite sure what you are looking for here, or if AME is the appropriate tool. The primary

Jul 31

Donny Hoang, … tlawb...@gmail.com4

Jul 30

Understanding MEME sites and FIMO hits

There is currently no way to easily extract the locations of the "scanned sites", or the

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Understanding MEME sites and FIMO hits

There is currently no way to easily extract the locations of the "scanned sites", or the

Jul 30

ara...@bu.edu, … tlawb...@gmail.com4

Jul 30

Does the number of query or target motifs affect the Tomtom p-value?

If the scientific question is "which of two motifs better matches motif X", then you would

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Does the number of query or target motifs affect the Tomtom p-value?

If the scientific question is "which of two motifs better matches motif X", then you would

Jul 30

Aastha Pal, cegrant2

Jul 3

You don't mention which of the MEME Suite tools you were using. I'm guessing it was either

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You don't mention which of the MEME Suite tools you were using. I'm guessing it was either

Jul 3

zealot, … cegrant6

Jun 8

Bad format "Invalid BED file" Line 1: sequence chrI not found in genome database.

Note that each sequence specified by your BED file is only two positions long, 112224825-112224827

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Bad format "Invalid BED file" Line 1: sequence chrI not found in genome database.

Note that each sequence specified by your BED file is only two positions long, 112224825-112224827

Jun 8

Ariana Treat, cegrant2

May 30

STREME Position Distribution Alignment

Are all your sequences the same length? That would explain why changing the alignment option wouldn

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STREME Position Distribution Alignment

Are all your sequences the same length? That would explain why changing the alignment option wouldn

May 30

Angus Hilts, cegrant2

May 23

Retaining all contributing sites from command line run of MEME

Have you looked at the -nsites -minsites, and -maxsites options described in the MEME documentation?

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Retaining all contributing sites from command line run of MEME

Have you looked at the -nsites -minsites, and -maxsites options described in the MEME documentation?

May 23

Corbin Machatzke, cegrant2

May 12

Motif discovery with ssDNA

STREME doesn't explicitly support scanning only one strand of DNA sequences but as you can

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Motif discovery with ssDNA

STREME doesn't explicitly support scanning only one strand of DNA sequences but as you can

May 12

Arthur Roque Justino, cegrant2

May 10

Differentially enriched motifs with different promoter sizes

The purpose of STREME is de novo motif discovery. Motif enrichment analysis with known motifs is

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Differentially enriched motifs with different promoter sizes

The purpose of STREME is de novo motif discovery. Motif enrichment analysis with known motifs is

May 10

inder jeet, cegrant2

Apr 26

The papers for all of the MEME Suite tools are listed here. The most useful for a general overview is

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The papers for all of the MEME Suite tools are listed here. The most useful for a general overview is

Apr 26

Mar 31

MAST hit_list score meaning

Thanks for clarifying what you are trying to do. As far as the computation of the motif match scores

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MAST hit_list score meaning

Thanks for clarifying what you are trying to do. As far as the computation of the motif match scores

Mar 31

Mar 19

MAST hit_list strand meaning

The columns in the hit list output are described in the documentation for the MAST command line in

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MAST hit_list strand meaning

The columns in the hit list output are described in the documentation for the MAST command line in

Mar 19

Kaustav Mukherjee, cegrant2

Mar 19

bad sequence identifier error: meme-chip in discriminative mode

Each sequence in the sequence database needs to have a unique name, but because there may be

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bad sequence identifier error: meme-chip in discriminative mode

Each sequence in the sequence database needs to have a unique name, but because there may be

Mar 19

Aastha Pal, cegrant2

Mar 10

meme-suite@uw.edu

Aastha, If you have not already fixed the problem with your BED file, here are some suggestions.

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meme-suite@uw.edu

Aastha, If you have not already fixed the problem with your BED file, here are some suggestions.

Mar 10

Aastha Pal, cegrant2

Mar 10

If you have not already fixed the problem with your BED file, here are some suggestions. Rather than

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If you have not already fixed the problem with your BED file, here are some suggestions. Rather than

Mar 10

Mar 10

MCAST Segmentation fault (core dumped)

While we don't currently support a Conda or Bioconda package, we do provide a MacPorts package

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MCAST Segmentation fault (core dumped)

While we don't currently support a Conda or Bioconda package, we do provide a MacPorts package

Mar 10

Dushyant Deotale, cegrant2

Jan 15

make test crash

If you look in the tests/scripts directory you should find log files for each of the tests. These

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make test crash

If you look in the tests/scripts directory you should find log files for each of the tests. These

Jan 15

Roberto Avellino, cegrant2

12/9/24

Searching for two adjacent motifs in a list of input sequences

I don't think the MEME Suite has a tool that does exactly what you seem to be asking for. SpaMo

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Searching for two adjacent motifs in a list of input sequences

I don't think the MEME Suite has a tool that does exactly what you seem to be asking for. SpaMo

12/9/24

alan.tou...@gmail.com, cegrant2

12/5/24

Explanation for STREME site_distr

For each motif it identifies, STREME first makes a list of the highest scoring occurrence of that

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Explanation for STREME site_distr

For each motif it identifies, STREME first makes a list of the highest scoring occurrence of that

12/5/24

Konrad Taube, cegrant5

10/16/24

Difficulty with GOMo

Konrad, One further thought. If you actually are not interested in the association between motifs and

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Difficulty with GOMo

Konrad, One further thought. If you actually are not interested in the association between motifs and

10/16/24

Gnéré Mariame Coulibaly, cegrant2

9/26/24

outputs of different version of MEME suite

You can consult the release notes to see what changes have been made to the MEME Suite tools. It

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outputs of different version of MEME suite

You can consult the release notes to see what changes have been made to the MEME Suite tools. It

9/26/24

Bhanu Sharma, cegrant2

9/25/24

STREME and MEME, result.

It's important to keep in mind that neither MEME or STREME are performing an exhaustive search

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STREME and MEME, result.

It's important to keep in mind that neither MEME or STREME are performing an exhaustive search

9/25/24

Qian Qiu, tlawb...@gmail.com2

9/15/24

The fimo.gff file was not accepted by the UCSC Genome Table Browser

Hi erzach, It appears your GFF file has been processed or corrupted in some way. Maybe someone cut-

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The fimo.gff file was not accepted by the UCSC Genome Table Browser

Hi erzach, It appears your GFF file has been processed or corrupted in some way. Maybe someone cut-

9/15/24

Gianluca Mattei, … cegrant4

9/9/24

GOMo pipeline clarification

Hi Gianluca, The GO term database (the first required argument to GOMO) maps sequences to the GO

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GOMo pipeline clarification

Hi Gianluca, The GO term database (the first required argument to GOMO) maps sequences to the GO

9/9/24

Amira Kramdi, cegrant2

9/9/24

Questions about creating epigenetic priors for FIMO (psp)

Is there a recommended resolution for the input wiggle file used for create-priors ? Does it have an

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Questions about creating epigenetic priors for FIMO (psp)

Is there a recommended resolution for the input wiggle file used for create-priors ? Does it have an

9/9/24

Fathima Ashraf, cegrant2

8/13/24

At their root STREME and MEME are identifying short, similar subsequences that are statistically

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At their root STREME and MEME are identifying short, similar subsequences that are statistically

8/13/24

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