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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...

0 selected

Laura Pineda, cegrant6

6/9/20

Order of input motifs affect MAST output

Thank you for the advice, I'll try to use FIMO.

unread,

motif_discovery

Order of input motifs affect MAST output

Thank you for the advice, I'll try to use FIMO.

6/9/20

Laura Pineda, cegrant4

5/28/20

MEME's motifs have an E-vaue too high

I'd suggest a few things. First, since you are looking for a known promoter you might consider

unread,

motif_discovery

MEME's motifs have an E-vaue too high

I'd suggest a few things. First, since you are looking for a known promoter you might consider

5/28/20

Skyler, … Joel Wallenius6

3/19/20

meme -p incompatible with (my) bash while loops?

Thank you Joel. That is more precise/concise and it solves the problem. Expert or no, I appreciate

unread,

motif_discovery

meme -p incompatible with (my) bash while loops?

Thank you Joel. That is more precise/concise and it solves the problem. Expert or no, I appreciate

3/19/20

Mathilde Perez, cegrant3

11/9/18

how to generate meme index file without installing the MEME Suite Web Application

Thanks for the quick reply! In the same time I figured out that indeed this file is need for Bagfoot

unread,

motif_discovery

how to generate meme index file without installing the MEME Suite Web Application

Thanks for the quick reply! In the same time I figured out that indeed this file is need for Bagfoot

11/9/18

Ashwini Jeggari, CharlesEGrant2

10/22/18

uniprobe pwm to meme format

I tried to run the script using single file. perl uniprobe2meme.pl.in uniprobe_Peterson2012_PWM/Gli1/

unread,

motif_discovery

uniprobe pwm to meme format

I tried to run the script using single file. perl uniprobe2meme.pl.in uniprobe_Peterson2012_PWM/Gli1/

10/22/18

Robert Leach, cegrant2

3/7/18

Why is this command stopping after finding 1 motif?

You need to specify the number of motifs you want MEME to find, using the '-nmotifs' option.

unread,

motif_discovery

Why is this command stopping after finding 1 motif?

You need to specify the number of motifs you want MEME to find, using the '-nmotifs' option.

3/7/18

Robert Leach, cegrant2

3/5/18

How to weight sequences in dreme?

I'm afraid any motif that involves an inexact match is going to be washed out in your data. With

unread,

motif_discovery

How to weight sequences in dreme?

I'm afraid any motif that involves an inexact match is going to be washed out in your data. With

3/5/18

Bharata Kalbuaji, CharlesEGrant2

2/22/18

Getting background from p-value and score

The background frequencies used are recorded in the FIMO XML and HTML output, but not in the plain

unread,

motif_discovery

Getting background from p-value and score

The background frequencies used are recorded in the FIMO XML and HTML output, but not in the plain

2/22/18

mdok...@fiu.edu, CharlesEGrant2

2/12/18

MEME-ChIP results interpretation

It looks like the masking of short repeats was incomplete. You don't mention what tool you used

unread,

motif_discovery

MEME-ChIP results interpretation

It looks like the masking of short repeats was incomplete. You don't mention what tool you used

2/12/18

Joel Wallenius, CharlesEGrant3

1/19/18

nsites lower than the number of sequences despite using OOPS

I would but I already removed all output and re-ran everything. I can't replicate the issue, it

unread,

motif_discovery

nsites lower than the number of sequences despite using OOPS

I would but I already removed all output and re-ran everything. I can't replicate the issue, it

1/19/18

Joel Wallenius, CharlesEGrant4

1/18/18

Is there a way to tell MEME to search for motifs that are similar to a specific (supplied on input) sequence?

Will it make MEME blind to motifs that are not similar to this consensus sequence? Blind is too

unread,

motif_discovery

Is there a way to tell MEME to search for motifs that are similar to a specific (supplied on input) sequence?

Will it make MEME blind to motifs that are not similar to this consensus sequence? Blind is too

1/18/18

Joel Wallenius, CharlesEGrant5

1/8/18

MEME stops without errors after finding the first motif

You can treat the E-value a p-value controlled for the size of the input sequence data. The

unread,

motif_discovery

MEME stops without errors after finding the first motif

You can treat the E-value a p-value controlled for the size of the input sequence data. The

1/8/18

Joel Wallenius, CharlesEGrant5

12/27/17

The minsites option does not work?

Thank you Charles!

unread,

motif_discovery

The minsites option does not work?

Thank you Charles!

12/27/17

Bharata Kalbuaji, CharlesEGrant3

5/25/17

Calculation of multiple matrix FDR

I see thank you very much. Now it becomes clear to me.

unread,

motif_discovery

Calculation of multiple matrix FDR

I see thank you very much. Now it becomes clear to me.

5/25/17

gatla, CharlesEGrant3

5/16/17

MEME de-novo motif discovery - parameters

1. I am centering the peaks of my interest and trying to call denovo motifs with different flanking

unread,

fasta-get-markov

motif_discovery

MEME de-novo motif discovery - parameters

1. I am centering the peaks of my interest and trying to call denovo motifs with different flanking

5/16/17

Arun Prasanna, CharlesEGrant2

2/11/17

ceqlogo error "No motifs were specified"

Here is the documentation for the ceqlogo command: http://meme-suite.org/doc/ceqlogo.html You have to

unread,

motif_discovery

ceqlogo error "No motifs were specified"

Here is the documentation for the ceqlogo command: http://meme-suite.org/doc/ceqlogo.html You have to

2/11/17

Arun Prasanna, CharlesEGrant2

1/16/17

Unable to get a statistically significant motif

The traditional threshold for a significant p-value or value is 0.01 or 0.05. While this is only a

unread,

motif_discovery

Unable to get a statistically significant motif

The traditional threshold for a significant p-value or value is 0.01 or 0.05. While this is only a

1/16/17

Arun Prasanna, CharlesEGrant2

1/5/17

Query on MEME sites

MEME is also a greedy algorithm, so as soon as it has enough information to estimate the statistical

unread,

motif_discovery

Query on MEME sites

MEME is also a greedy algorithm, so as soon as it has enough information to estimate the statistical

1/5/17

Rajan Joshi, CharlesEGrant2

1/4/17

Interpreting glam2 score significance

Glam2 doesn't provide a built in statistical significance estimate for the motifs it discovers.

unread,

motif_discovery

Interpreting glam2 score significance

Glam2 doesn't provide a built in statistical significance estimate for the motifs it discovers.

1/4/17

Nicolas Descostes, CharlesEGrant2

12/29/16

problem with motif length meme-chip

Hmm. You've set the -meme-minw and -meme-maxw options appropriately. Are the motifs identified by

unread,

motif_discovery

problem with motif length meme-chip

Hmm. You've set the -meme-minw and -meme-maxw options appropriately. Are the motifs identified by

12/29/16

Arun Prasanna, CharlesEGrant4

12/30/16

Query on MEME for large dataset

That sounds about right. You want to provide MEME with multiple sequences that you think contain

unread,

motif_discovery

Query on MEME for large dataset

That sounds about right. You want to provide MEME with multiple sequences that you think contain

12/30/16

Aoi Summer, CharlesEGrant2

11/7/16

Limit of FIMO ouput

Using a p-value threshold when scanning an entire genome runs into the problem of multiple testing.

unread,

motif_discovery

Limit of FIMO ouput

Using a p-value threshold when scanning an entire genome runs into the problem of multiple testing.

11/7/16

Nicolas Descostes, CharlesEGrant3

10/10/16

motif, e-value and number of sequences

Thank you very much Charles and sorry for cross posting.

unread,

motif_discovery

motif, e-value and number of sequences

Thank you very much Charles and sorry for cross posting.

10/10/16

Rocky Parida, CharlesEGrant3

9/12/16

MEME motif discovery

Hi Charles Based on your answer -revcomp is not set as default by meme command line version but only

unread,

motif_discovery

MEME motif discovery

Hi Charles Based on your answer -revcomp is not set as default by meme command line version but only

9/12/16

Raymond Wan, CharlesEGrant7

4/28/16

Dreme masking and sequence length

Hi Charles, On Tuesday, 26 April 2016 05:43:32 UTC+8, CharlesEGrant wrote: Hi Ray, What I was

unread,

motif_discovery

Dreme masking and sequence length

Hi Charles, On Tuesday, 26 April 2016 05:43:32 UTC+8, CharlesEGrant wrote: Hi Ray, What I was

4/28/16

R. Biot, CharlesEGrant2

3/21/16

Peculiar case: MEME or MEME-ChIP?

The primary resource for MEME-ChIP procedural questions is this paper: Wenxiu Ma, William Stafford

unread,

motif_discovery

Peculiar case: MEME or MEME-ChIP?

The primary resource for MEME-ChIP procedural questions is this paper: Wenxiu Ma, William Stafford

3/21/16

Kelian Hacid, cegrant5

7/16/15

How does MEME react while changing the input motif size and/or the input background

Ok thank you Charles !

unread,

motif_discovery

How does MEME react while changing the input motif size and/or the input background

Ok thank you Charles !

7/16/15

ndcu...@gmail.com, James Johnson5

4/20/15

MEME-ChiP for 50bp sequences

Thanks James :)

unread,

motif_discovery

MEME-ChiP for 50bp sequences

Thanks James :)

4/20/15

Roberto, James Johnson2

1/26/15

xml to html bug on v.4.10.0_2

Patch 3 fixes this problem. I had hoped that the people running the download server would have put it

unread,

motif_discovery

xml to html bug on v.4.10.0_2

Patch 3 fixes this problem. I had hoped that the people running the download server would have put it

1/26/15

Gonzalo Sepulveda, CharlesEGrant2

5/21/14

How to validate meme's suite results

What is it you are trying to validate? If you are just trying to validate that the tools are

unread,

motif_discovery

How to validate meme's suite results

What is it you are trying to validate? If you are just trying to validate that the tools are

5/21/14

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