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MEME Suite Q&A

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Welcome to the MEME Suite question and answer forum.

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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4/2/19

The basics of using MEME to discover motifs

MEME is a tool for performing de novo motif discovery in DNA, RNA, and proteins. This is a very brief

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The basics of using MEME to discover motifs

MEME is a tool for performing de novo motif discovery in DNA, RNA, and proteins. This is a very brief

4/2/19

4/17/18

How do I use MEME suite for searching for motifs?

Note that this post only covers some of the most commonly used tools in the MEME Suite but then if

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motif_discovery

How do I use MEME suite for searching for motifs?

Note that this post only covers some of the most commonly used tools in the MEME Suite but then if

4/17/18

aishwarya kulkarni, cegrant2

6/2/20

Can't locate HtmlMonolithWr.pm

I responded to your other posting.

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Can't locate HtmlMonolithWr.pm

I responded to your other posting.

6/2/20

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

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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

Trevor C, cegrant2

5/12/20

-evt argument in meme not working.

The problem is that MEME is a greedy algorithm and is not guaranteed to identify motifs in strictly

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-evt argument in meme not working.

The problem is that MEME is a greedy algorithm and is not guaranteed to identify motifs in strictly

5/12/20

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

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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

Yusuke Takahashi

3/12/20

[Enhancement] The default value of maxsites of meme is confusing

Dear All, Under some conditions, "maxsites" is cut off at 1000. This behavior, I think, is

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[Enhancement] The default value of maxsites of meme is confusing

Dear All, Under some conditions, "maxsites" is cut off at 1000. This behavior, I think, is

3/12/20

Yusuke Takahashi, cegrant4

3/28/20

meme may return floating number maxsites, which causes an error in meme_xml_to_html

Hi Yusuke, I'm not familiar with the protocols for working with DNA modification loci, and so I

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meme may return floating number maxsites, which causes an error in meme_xml_to_html

Hi Yusuke, I'm not familiar with the protocols for working with DNA modification loci, and so I

3/28/20

Pushya Krishna, cegrant2

8/20/19

Entire test either skipped or failed?

how can I get meme2meme and the other motif format utilities to work? Users had pointed out to us

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Entire test either skipped or failed?

how can I get meme2meme and the other motif format utilities to work? Users had pointed out to us

8/20/19

Kashif Nawaz, CharlesEGrant2

3/13/19

Convert Fasta format to MEME-motif format

Assuming you have the MEME suite installed on your computer, you have access to the scripts here:

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Convert Fasta format to MEME-motif format

Assuming you have the MEME suite installed on your computer, you have access to the scripts here:

3/13/19

2/13/19

AME perl python output issue

By using AME with the following command, the output is similar to the online version but I do not

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AME perl python output issue

By using AME with the following command, the output is similar to the online version but I do not

2/13/19

11/27/18

How to create priors from ATAC-seq data for FIMO

The documentation for the create-priors script can be found here: http://meme-suite.org/doc/create-

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How to create priors from ATAC-seq data for FIMO

The documentation for the create-priors script can be found here: http://meme-suite.org/doc/create-

11/27/18

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/

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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

Nick Riddiford, CharlesEGrant3

7/24/18

Enrichment of de-novo discovered motifs

Hi Charles, Thanks a lot for your very helpful and detailed response. We are looking for motifs

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Enrichment of de-novo discovered motifs

Hi Charles, Thanks a lot for your very helpful and detailed response. We are looking for motifs

7/24/18

jiecon...@gmail.com, CharlesEGrant2

7/10/18

/bin/bash: compile: command not found when using MAKE

The "compile not found" message ndicates that you don't have the Java build tool, ant,

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/bin/bash: compile: command not found when using MAKE

The "compile not found" message ndicates that you don't have the Java build tool, ant,

7/10/18

jiecon...@gmail.com, CharlesEGrant2

7/5/18

Question about update-sequence-db --ucsc

Thanks for letting us know about the problem. We're always in a race to keep up with changes to

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Question about update-sequence-db --ucsc

Thanks for letting us know about the problem. We're always in a race to keep up with changes to

7/5/18

Sarah Lerch, … CharlesEGrant3

4/17/18

MEME errors: 'psp_sum > 0' failed and (core dumped)

Could you attach or forward us a copy of the input sequences? That would help us troubleshoot the

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MEME errors: 'psp_sum > 0' failed and (core dumped)

Could you attach or forward us a copy of the input sequences? That would help us troubleshoot the

4/17/18

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.

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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

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

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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

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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

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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

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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

Alex Reynolds, CharlesEGrant3

6/14/17

Required system property X509_USER_PROXY not set

First, version 4.11.0 is a bit old. The current version of the MEME Suite is 4.11.4. This is probably

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Required system property X509_USER_PROXY not set

First, version 4.11.0 is a bit old. The current version of the MEME Suite is 4.11.4. This is probably

6/14/17

Hiko Wong, CharlesEGrant2

5/16/17

MEME suite install error

If you look in the file tests/scripts/dreme.log you should find detailed information about why the

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MEME suite install error

If you look in the file tests/scripts/dreme.log you should find detailed information about why the

5/16/17

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

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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

Varsha Sundaresan, CharlesEGrant5

2/21/17

meme mast overlapping motif search

HI Charles, I will try out FIMO. Thank you so much!

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meme mast overlapping motif search

HI Charles, I will try out FIMO. Thank you so much!

2/21/17

Santhilal Subhash, CharlesEGrant2

2/20/17

Installation Error (CRASH)

In the linked log all of the failures are associated with this error message: /usr/bin/perl: symbol

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Installation Error (CRASH)

In the linked log all of the failures are associated with this error message: /usr/bin/perl: symbol

2/20/17

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

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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

Varsha Sundaresan, CharlesEGrant3

1/12/17

How to get mast meme output as bed format file

I just found out the command to get the bed format was use -hit_list in the command line option with

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How to get mast meme output as bed format file

I just found out the command to get the bed format was use -hit_list in the command line option with

1/12/17

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

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