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Discovering Novel Sequence Motifs with MEME
Publication Name:
Current Protocols in Bioinformatics
Unit Number:
Unit 2.4
DOI:
10.1002/0471250953.bi0204s00
Online Posting Date:
January, 2003 Abstract
This unit illustrates how to use MEME to discover motifs in a group of related nucleotide or peptide sequences. A MEME motif is a sequence pattern that occurs repeatedly in one or more sequences in the input group. MEME can be used to discover novel patterns because it bases its discoveries only on the input sequences, not on any prior knowledge (such as databases of known motifs). The input to MEME is a set of unaligned sequences of the same type (peptide or nucleotide). For each motif it discovers, MEME reports the occurrences (sites), consensus sequence, and the level of conservation (information content) at each position in the pattern. MEME also produces block diagrams showing where all of the discovered motifs occur in the training set sequences. MEME's hypertext (HTML) output also contains buttons that allow for the convenient use of the motifs in other searches.
Table of Contents
- Unit Introduction
- Basic Protocol 1: Discovering Motifs in a Protein Sequence Family Using MEME
- Support Protocol: Searching for Other Proteins Containing the Same Motifs
- Alternate Protocol 1: Finding Repeated Motifs in Protein Sequences
- Basic Protocol 2: Discovering DNA Motifs in a set of DNA Sequences with MEME
- Alternate Protocol 2: Finding Repeated Motifs in DNA Sequences with MEME
- Guidelines for Understanding Results
- Commentary
- Literature Cited
- Figures
- Tables
Materials
Basic Protocol 1: Discovering Motifs in a Protein Sequence Family Using MEME
Necessary Resources
- Hardware
- Computer connected to the InternetCommand-line MEME works on many uniprocessor computers, some multiprocessor computers, and clusters that have the MPICH message-passing software installed. A list of supported operating systems and their manufacturers is available at ftp://ftp.sdsc.edu/pub/sdsc/biology/meme/README.
- Software
- Web browser (e.g., Internet Explorer, Netscape Navigator)
- E-mail reader (e.g., Netscape Messenger)
- Command-line MEME (optional) (http://meme.sdsc.edu/meme/website/meme-download.html)
MEME can be used remotely over the Web (Web MEME), with results being returned by E-mail, or it can be installed and run on the user's Unix-based computer (command-line MEME). The Web interface has the advantage of not requiring any software installation, but some MEME features are only available in the command-line version. Command-line MEME removes the restriction on the size of the training set imposed by the MEME Web server (maximum of 60,000 characters). Web access is free (currently available at http://meme.sdsc.edu and http://bioweb.pasteur.fr/seqanal/motif/meme). The command-line version is free for noncommercial use or can be obtained with a commercial license, and can be downloaded over the Web (http://meme.sdsc.edu/meme/website/meme-download.html).
When using MEME via a Web interface, results will typically arrive within a few hours. It is not possible to predict when the MEME results will arrive because the computers on which MEME runs at SDSC and the Pasteur Institute are shared resources. Depending on the load, it can sometimes take a day or more for a job to be processed. Please be patient. This unpredictability can be avoided by installing command-line MEME locally on the user's Unix-based computer.
- Files
- A sequence file (training set) containing one or more protein sequences (
There are many ways to construct a family of protein sequences for input to MEME. For example, file tf4.fasta contains a family of bacterial protein sequences related to Entrez sequence gi|15897224|ref|NP_341829.1| hypothetical protein [Sulfolobus solfataricus]. It was constructed by doing aThe data file used in this example (tf4.fasta) should be downloaded from the Current Protocols Web site (http://www3.interscience.wiley.com/c_p/cpbi_sampledatafiles.htm).
Support Protocol: Searching for Other Proteins Containing the Same Motifs
Necessary Resources
- Hardware
- Computer connected to the Internet
- Software
- Web browser (e.g., Internet Explorer, Netscape Navigator)
- E-mail reader (e.g., Netscape Messenger)
- Files
- Results from MEME (see
Alternate Protocol 1: Finding Repeated Motifs in Protein Sequences
Necessary Resources
- Hardware
- Computer connected to the Internet
- Command-line MEME works on many uniprocessor computers, some multiprocessor computers, and clusters that have the MPICH message-passing software installed. A list of supported operating systems and their manufacturers is available at: ftp://ftp.sdsc.edu/pub/sdsc/biology/meme/README.
- Software
- Web browser (e.g., Internet Explorer, Netscape Navigator)
- E-mail reader
- Command-line MEME (optional)
- MEME can be used remotely over the Web (Web MEME), with results being returned by E-mail, or it can be installed and run on the user's Unix-based computer (command-line MEME). The Web interface has the advantage of not requiring any software installation, but some MEME features are only available in the command-line version. Command-line MEME removes the restriction on the size of the training set imposed by the MEME Web server (maximum of 60,000 characters). Web access is free (currently available at http://meme.sdsc.edu and http://bioweb.pasteur.fr/seqanal/motif/meme). The command-line version is free for noncommercial use or can be obtained with a commercial license, and can be downloaded over the Web (http://meme.sdsc.edu/meme/website/meme-download.html).
- When using MEME via a Web interface, results will typically arrive within a few hours. It is not possible to predict when the MEME results will arrive because the computers on which MEME runs at SDSC and the Pasteur Institute are shared resources. Depending on the load, it can sometimes take a day or more for a job to be processed. Please be patient. This unpredictability can be avoided by installing command-line MEME locally on the user's Unix-based computer.
- Files
- A sequence file (the training set) containing one or more protein sequences. Note that sequences must be in
There are many ways to construct a family of protein sequences for input to MEME. For example, file tf4.fasta contains a family of bacterial protein sequences related to Entrez sequence gi|15897224|ref|NP_341829.1|, hypothetical protein [Sulfolobus solfataricus]. It was constructed by doing a BLASTP search of the nonredundant protein database (unit 3.4 ) using the sequence named above (gi|15897224) as the query. The accession numbers of all of the sequences matching the query with BLAST E-values £0.01 were then placed in file tf4.acc. Then, Batch Entrez (unit 1.3 ) was used with the file of accession numbers to download the sequences in FASTA format into file tf4.fasta.
The data file (tf4.fasta) used in this example should be downloaded from the Current Protocols Web site (http://www3.interscience.wiley.com/c_p/cpbi_sampledatafiles.htm).
Basic Protocol 2: Discovering DNA Motifs in a set of DNA Sequences with MEME
Necessary Resources
- Hardware
- Computer connected to the Internet
- Command-line MEME works on many uniprocessor computers, some multiprocessor computers, and clusters that have the MPICH message-passing software installed. A list of supported operating systems and their manufacturers is available at ftp://ftp.sdsc.edu/pub/sdsc/biology/meme/README (optional).
- Software
- Web browser (e.g. Internet Explorer, Netscape Navigator)
- E-mail reader
- Command-line MEME (optional)
- Files
- A sequence file (the training set) containing one or more protein sequences
MEME can be used remotely over the Web (Web MEME), with results being returned by E-mail, or it can be installed and run on the user's Unix-based computer (command-line MEME). The Web interface has the advantage of not requiring any software installation, but some MEME features are only available in the command-line version. Command-line MEME removes the restriction on the size of the training set imposed by the MEME Web server (maximum of 60,000 characters). Web access is free (currently available at http://meme.sdsc.edu and http://bioweb.pasteur.fr/seqanal/motif/meme). The command-line version is free for noncommercial use or can be obtained with a commercial license, and can be downloaded over the Web (http://meme.sdsc.edu/meme/website/meme-download.html).
When using MEME via a Web interface, results will typically arrive within a few hours. It is not possible to predict when the MEME results will arrive because the computers on which MEME runs at SDSC and the Pasteur Institute are shared resources. Depending on the load, it can sometimes take a day or more for a job to be processed. Please be patient. This unpredictability can be avoided by installing command-line MEME locally on the user's Unix-based computer.
Note that sequences must be in FASTA format (appendix 1B ) if using command-line MEME. Other formats, described on the MEME Web site, are supported if using MEME via the Web interface, but the total number of characters in the sequences may not exceed 60,000.
There are many ways to construct a set of DNA sequences for input into MEME—e.g., a set of upstream regions from genes known to be co-regulated as determined by expression microarray experiments can be used. In this example, a file (lex.fasta) will be used that contains a set of E. coli DNA sequences known to bind LexA. MEME will be used to discover the LexA binding sites and characterize the motif.
The data file (lex.fasta) used in this example should be downloaded from the Current Protocols Web site (http://www3.interscience.wiley.com/c_p/cpbi_sampledatafiles.htm).
Alternate Protocol 2: Finding Repeated Motifs in DNA Sequences with MEME
Necessary Resources
- Hardware
- Computer connected to the Internet
- Command-line MEME works on many uniprocessor computers, some multiprocessor computers, and clusters that have the MPICH message-passing software installed. A list of supported operating systems and their manufacturers is available at ftp://ftp.sdsc.edu/pub/sdsc/biology/meme/README (optional).
- Software
- Web browser (e.g. Internet Explorer, Netscape Navigator)
- E-mail reader
- Command-line MEME (optional)
- Files
- A sequence file (the training set) containing one or more DNA sequences
MEME can be used remotely over the Web (Web MEME), with results being returned by E-mail, or it can be installed and run on the user's Unix-based computer (command-line MEME). The Web interface has the advantage of not requiring any software installation, but some MEME features are only available in the command-line version. Command-line MEME removes the restriction on the size of the training set imposed by the MEME Web server (maximum of 60,000 characters). Web access is free (currently available at http://meme.sdsc.edu and http://bioweb.pasteur.fr/seqanal/motif/meme). The command-line version is free for noncommercial use or can be obtained with a commercial license, and can be downloaded over the Web (http://meme.sdsc.edu/meme/website/meme-download.html).
When using MEME via a Web interface, results will typically arrive within a few hours. It is not possible to predict when the MEME results will arrive because the computers on which MEME runs at SDSC and the Pasteur Institute are shared resources. Depending on the load, it can sometimes take a day or more for a job to be processed. Please be patient. This unpredictability can be avoided by installing command-line MEME locally on the user's Unix-based computer.
Note that sequences must be in FASTA format (appendix 1B ) if using command-line MEME. Other formats, described on the MEME Web site, are supported if using MEME via the Web interface, but the total number of characters in the sequences may not exceed 60,000.
This example uses a file (INO_up800.fasta) that contains upstream regions from S. cerevisiae genes known to be repressed in the presence of inositol or choline (van Helden et al., 1998 ).
The file (INO_up800.fasta) used in this example should be downloaded from the Current Protocols Web site (http://www3.interscience.wiley.com/c_p/cpbi_sampledatafiles.htm).
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Figures
-
Figure 2.4.1Overview of the input and output of MEME. -
Figure 2.4.2A typical protein motif discovered by MEME showing the aligned motif sites, multilevel consensus sequence, and information content. -
Figure 2.4.3A typical Summary of Motifs diagram produced by MEME showing the positions of occurrences of the three motifs MEME discovered. The names of the training set sequences and a measure of how well all three motifs are represented in each sequence (combined P-value) are shown to the left of each. -
Figure 2.4.4MEME input form for the tf4 protein family assuming zero or one occurrence of a single motif in each sequence. -
Figure 2.4.5MEME verification screen. -
Figure 2.4.6MEME confirmation E-mail message. -
Figure 2.4.7MEME E-mail results header. The actual results are attached to the E-mail message as an HTML attachment. Many E-mail programs display the attachment directly, but it is usually better to save the attachment to a file and use a web browser to view it. -
Figure 2.4.8Six buttons at the top of the MEME output, which allow for easy navigation through the file. -
Figure 2.4.9MEME command-line summary section showing all the MEME parameters. This is useful for keeping track of distinct MEME runs. -
Figure 2.4.10MEME training set section. -
Figure 2.4.11Motif summary line. -
Figure 2.4.12Simplified PSPM, information content diagram, consensus, and alignment. -
Figure 2.4.13Motif 5 block diagrams showing schematically the position and strength of occurrences of motif 5 in the training set. -
Figure 2.4.14The figure displays the options available under the Motif 5 in BLOCKS format. The user may choose to view the motif in block, FASTA, or raw format by clicking the appropriate button. The Submit BLOCK 5 button provides a link to the Blocks database (unit -
Figure 2.4.15A display of Motif 5 in FASTA Format, obtained by clicking on the View FASTA 5 button shown in Figure -
Figure 2.4.16Motif 5 in Logos format obtained by clicking on the Submit Block 5 button shown in Figure -
Figure 2.4.17Motif 5 neighbor-joining tree obtained by clicking on the Submit Block 5 button shown in Figure -
Figure 2.4.18Motif 5 neighbor-joining tree obtained by clicking on the Submit Block 5 button shown in Figure -
Figure 2.4.19Summary of motifs diagram showing the positions of matches to all ten motifs discovered by MEME in the training set. The diagram is generated by searching for all nonoverlapping matches to the motif PSSMs, and may not correspond exactly to the individual motif block diagrams (e.g., Fig. -
Figure 2.4.20Top of MAST input form showing all of the required inputs—i.e., the user's E-mail address and the sequence to search. -
Figure 2.4.21Partial results of a MAST search of yeast showing the motif matches in schematic format. -
Figure 2.4.22MetaMEME input form. -
Figure 2.4.23MetaMEME search of yeast. -
Figure 2.4.24MEME input form for the tf4 protein family assuming any number of repeats of a single motif in each sequence. -
Figure 2.4.25MEME motif summary: repeated motifs. -
Figure 2.4.26LAMA search of BLOCKS motif database showing the top matches of the MEME motifs to known protein motifs. -
Figure 2.4.27Neighbor-joining tree of motif 1. -
Figure 2.4.28MAST search of yeast with repeated motifs. -
Figure 2.4.29MEME input form for LexA binding sites. -
Figure 2.4.30LexA binding site motif. -
Figure 2.4.31Summary of motifs in lex.fasta. A minus sign before the motif number indicates that the match is on the reverse complement strand. A plus sign indicates that the motif is on the given strand. -
Figure 2.4.32MAST input form for LexA. -
Figure 2.4.33MAST results of search of E. coli with LexA binding site motif. -
Figure 2.4.34MEME input form for genes repressed by inositol or choline. -
Figure 2.4.35Inositol binding site motif identified by MEME.
Literature Cited
| Literature Cited | |
| Bailey, T.L. and Elkan, C. 1995. The value of prior knowledge in discovering motifs with MEME. In Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, pp. 21-29. AAAI Press, Menlo Park, Calif. | |
| Bailey, T.L. and Gribskov, M. 1998. Combining evidence using p-values: Application to sequence homology searches. Bioinform. 14:48-54. | |
| Grundy, W.N., Bailey, T.L., Elkan, C.P., and Baker, M.E. 1997. Meta-MEME: Motif-based hidden Markov models of protein families. Comp. Appl. Bio. Sci. 13:397-496. | |
| Kyte, J. and Doolittle, R. 1982. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157:105-132. | |
| Lawrence, C.E. and Reilly, A.A. 1990. An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Struc. Func. Genet. 7:41-50. | |
| Pietrokovski, S. 1996. Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucl. Acids Res. 24:3836-3845. | |
| Pietrokovski, S., Henikoff, S., and Henikoff, J. 1996. The BLOCKS database: A system for protein classification. Nucl. Acids Res. 24:197-200. | |
| van Helden, J., André, B., and Collado-Vides, J. 1998. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol. 281:827-942. | |
| Wingender, E., Chen, X., Hehl, R., Karas, H., Liebich, I., Matys, V., Meinhardt, T., Pruss, M., Reuter, I., and Schacherer, F. 2000. TRANSFAC: An integrated system for gene expression regulation. Nucl. Acids Res. 28:316-319. | |
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