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MEME Suite Q&A

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Welcome to the MEME Suite question and answer forum.

As of 12PM PST Nov. 3 2025 We've completed the restoration of the MEME Suite web site and it is available for public use again.

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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cegrant, … mitali gupta8

11/9/25

MEME Suite is down

Sincere thanks to the entire team for all their efforts and dedication. On Tuesday, November 4, 2025

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MEME Suite is down

Sincere thanks to the entire team for all their efforts and dedication. On Tuesday, November 4, 2025

11/9/25

Angus Hilts, … X L11

12/21/25

Retaining all contributing sites from command line run of MEME

Sorry the link is here https://drive.google.com/drive/folders/1Dcqja_QfmqyX8YmO-1BBy_7Xuw_KX-Ce?usp=

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Retaining all contributing sites from command line run of MEME

Sorry the link is here https://drive.google.com/drive/folders/1Dcqja_QfmqyX8YmO-1BBy_7Xuw_KX-Ce?usp=

12/21/25

12/17/25

Control set selection for STREME in short sequence enrichment analysis

Hi, I'm trying to find enriched sequence motifs from a large set of short sequences that are

unread,

Control set selection for STREME in short sequence enrichment analysis

Hi, I'm trying to find enriched sequence motifs from a large set of short sequences that are

12/17/25

10/6/25

Inquiry regarding MEME Suite website downtime

Dear MEME Suite Team It has been 11 days since the MEME Suite website is unavailable. could you

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Inquiry regarding MEME Suite website downtime

Dear MEME Suite Team It has been 11 days since the MEME Suite website is unavailable. could you

10/6/25

10/6/25

Inquiry regarding MEME Suite Website downtime

Dear MEME Suite Team It has been 11 days since the MEME Suite Website is unavailable. Now, could you

unread,

Inquiry regarding MEME Suite Website downtime

Dear MEME Suite Team It has been 11 days since the MEME Suite Website is unavailable. Now, could you

10/6/25

9/25/25

MEME Suite: inaccessible

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

unread,

MEME Suite: inaccessible

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

9/25/25

Pipistrellus, cegrant2

8/28/25

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

8/28/25

Xuan Wang, cegrant2

8/14/25

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

8/14/25

Elaine wu, cegrant2

7/31/25

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

7/31/25

XIYIN SHI, cegrant2

7/31/25

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

7/31/25

Donny Hoang, … tlawb...@gmail.com4

7/30/25

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

7/30/25

ara...@bu.edu, … tlawb...@gmail.com4

7/30/25

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

7/30/25

Aastha Pal, cegrant2

7/3/25

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

7/3/25

zealot, … cegrant6

6/8/25

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

6/8/25

Ariana Treat, cegrant2

5/30/25

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

5/30/25

Corbin Machatzke, cegrant2

5/12/25

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

5/12/25

Arthur Roque Justino, cegrant2

5/10/25

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

5/10/25

inder jeet, cegrant2

4/26/25

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

4/26/25

3/31/25

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

3/31/25

3/19/25

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

3/19/25

Kaustav Mukherjee, cegrant2

3/19/25

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

3/19/25

Aastha Pal, cegrant2

3/10/25

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.

3/10/25

Aastha Pal, cegrant2

3/10/25

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

3/10/25

3/10/25

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

3/10/25

Dushyant Deotale, cegrant2

1/15/25

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

1/15/25

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

unread,

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

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