MEME Suite System Release Notes
MEME version 4.2.0 -- June 22, 2009
- MEME --
MEME now can use position-specific priors (PSP) to improve motif discovery. The PSP is specified using the-psp pspfile
switch to MEME. - GOMO --
Added the ability to choose either maximum or average binding affinity as the scoring function.
Fixed a bug--was using maximum affinity by default, contrary to the documentation. - AMA --
AMA now computes p-value of each sequence based on a 0-order background model for the dataset.
Improved speed and memory efficiency; was re-reading sequences and storing them in memory.
Fixed bug--was using max-odds by default and the --scoring switch was being ignored. - MAST -- website now supports protein databases even when DNA database contains long sequences.
- Installation --
Now all programs in the MEME suite are built. The --enable-both configure switch is now obsolete.
Simplified the build process by removing support for separately building the tools formerly included in Meta-MEME.
Update on-line documentation.
Simplified "quick install" instructions are provided inINSTALL
and indoc/meme-install.html
.
MEME version 4.1.1
- Improved documentation.
- Increased default number of iterations for GLAM2.
- Improved error handling for sequence data.
- Added links to server activity summary.
- Fixed bug in install process when
--enable-both
not used.
MEME version 4.1.0
- New tool: GOMO -- Finding Genome Ontology terms associated with DNA binding motifs.
- Added FIMO and GOMO buttons to MEME output to make it easy to use discovered motifs to search sequence databases and to identify the role of DNA binding motifs.
- Fixed placement of sidebar menu in Internet Explorer for output of CGI scripts.
- Fixed support for OpenMPI in MEME.
- Improved the efficiency of FIMO.
-
Made the
-text
option to FIMO produce results on-the-fly, without sorting or q-values. This mode allows very large databases to be searched, without storing intermediate results. -
Modified the command line syntax for
gendb
, for consistency with the rest of the suite.
MEME version 4.0.0 -- June 13, 2008
- New Features and Enhancements
- MEME and Meta-MEME are now integrated as "The MEME Suite".
- New web-based tools:
- GLAM2 and GLAM2SCAN--discovery and scanning of gapped motifs
- Tomtom--comparing motifs
- FIMO--basic motif scanning (complements MAST)
- Enhancements of existing tools:
- Sequence LOGOS now enhance MEME output.
- Compare new motifs to databases of motifs via Tomtom by clicking an easy-to-use button on MEME and GLAM2 output.
- Improved local search (branching search) in MEME (command line version only).
- Hundreds of new genomic and upstream sequence databases are now supported for scanning by MAST, FIMO or GLAM2SCAN.
- Tomtom supports four motif databases: JASPAR, Transfac, SCPD and MacIsaac Yeast.
- The MEME Suite tools now have web servers powered by OPAL, and return their results via the web, rather than by email.
- A single web server portal simplifies different types of motif scanning tasks
MEME version 3.5.7 -- December 14, 2007
- New Features and Enhancements
- Parallel MEME is compiled when no scheduler is found but MPICH is detected.
- Opal integration with meme.
- Added --enable-webservice=<path_to_build-opal.xml> configure flag. Used to automate deployment of MEME inside an Opal installation as a web service.
- Added --enable-web=<opal_url> configure flag. Used to enable building of the MEME web portal. A URL for an Opal-exposed MEME web service must be entered.
MEME version 3.5.5 -- May 31, 2007
- New Features and Enhancements
- MAST -hit_list can now handle very long sequences and prints ALL hits regardless of the sequence E-value cutoff. It splits them into "swaths". The -hit_list switch now overrides the -seqp switch, and hits are NOT sorted by the E-value of the sequence.
MEME version 3.5.4 -- September 21, 2006
- New Features and Enhancements
- Changed the MAST -hit_list behavior to print ONLY a list
of the non-overlapping significant motif matches in each
sequence in a machine-readable format.
(More complete documentation is given in the MAST "usage"
message. Type "mast" on the UNIX command line to see the usage message.)
An example of the (complete) output of MAST using the -hit_list switch is:
# All non-overlapping hits in all sequences. # sequence_name motif hit_start hit_end score hit_p-value ce1cg -2 8 22 1459.90 1.67e-06 ara +2 2 16 1661.18 5.04e-08 bglr1 +2 1 15 1274.97 1.42e-05 cya -2 19 33 1101.37 6.64e-05 gale +2 5 19 1076.21 8.11e-05 ilv -2 6 20 1098.85 6.78e-05 malk +2 37 51 1085.02 7.56e-05 ompa +2 5 19 1583.18 2.43e-07 # mast tests/meme.crp0.oops tests/crp0.s -stdout -hit_list -m 2
- New "regular expression" section added to each MEME motif.
- Changed the MAST -hit_list behavior to print ONLY a list
of the non-overlapping significant motif matches in each
sequence in a machine-readable format.
(More complete documentation is given in the MAST "usage"
message. Type "mast" on the UNIX command line to see the usage message.)
An example of the (complete) output of MAST using the -hit_list switch is:
- Bug fixes
- Fixed printing of command name in MAST results.
- Fixed the handling of the "View FASTA", "View RAW" and "View motif summary" buttons on the MEME form.
- Improved documentation of the "Motif Summary" section of MEME output.
- Fixed bug that prevented having multiple MEME and MAST servers running on a single host by different users. Each server is distinguished by the socket number it listens on.
- Known Issues
- The "MetaMEME" button on the top of MEME results page is still not functional. Users are advised to go to the MetaMEME web site and submit manually at this time.
- MAST: Uploaded file names containg quotation marks may cause the search to fail.
- MAST: Uploaded sequences in DOS/Windows format may cause the search to fail.
MEME version 3.5.3 -- April 20, 2006
- New Features and Enhancements
- The capability to search three JASPAR databases of DNA motifs for matches to a MEME-discovered motif has been added to the MEME output form. Pressing the 'COMPARE PSPM' button on the results form of a MEME search of DNA sequences will submit the selected motif PSPM to the JASPAR 'Compare' server. This will allow you to determine if your motif is similar to any known motifs contained in one of the three JASPAR motif databases.
- Bug fixes
- The "MAST" button on the top of MEME results page now automatically loads the motifs from the MEME results for MAST search. A user only needs to choose the database (uploaded or server side) to search against.
MEME version 3.5.2 -- March 1, 2006
- New Features and Enhancements
- Newly designed web insterface using javascript and css styling.
- Add support for Macos X server startup.
- Add meme-install.html with detailed explanation of installation procedures.
- Bug fixes
- In "configure" remove check dependency on parallel condition when creating server executables.
- Path to images/ in cgi scripts.
- Description syntax in linux startup script meme.linux.
- Provide fix for a cygwin's new line representation when searching strings.
- Bug in e_step (oops.c)
- Bug caused by typo "MEME_BINbin"
- Remove use of min() in meme.pl
- Remove obsolete argument sample_prob from subseq7()
- Remove OS-dependent declarations of accept(), bind(), connect(), socket(), listen(), htons(). They are defined in system header files.
MEME version 3.5.1 -- December 15, 2005
-
Bug fixes
- Revert binary and scripts names to what they used to be in version prior to 3.5.0. The binary executables have an extension ".bin", and the shell scripts have their extension ".csh" removed. This allows to keep compatibility with earlier versions.
- Change startup scripts to start servers as a user specified during configuration. If none were specified, then the uid of the user who runs configure will be used.
- Always install files in etc/.
- Always install Globals.pm in lib/perl/.
- Move meme-explanation.html from web/html/ to etc/. This allows to run scripts that do conversion to html when web site is not installed.
-
Enhancements
- Added support for Macos X (serial verison only, without server)
- Users can now compare DNA motifs to the motifs in the JASPAR database of transcription factor binding site motifs. A button is provided in the PSPM section of each DNA motif on the MEME output form for this purpose. Clicking on the "Compare PSPM x to known motifs in JASPAR database" sends the motif to the JASPAR website, which returns any similar motifs that are found.
- Add meme_config.csh file that is used automatically by csh scripts to set needed environment variables.
- Move job.out file (created when SGE scheduler is used) to LOGS/
- Add '--with-serial' option to 'configure.ac' for compiling only serial version
- Disable installlation of web by default. To install use --with-web configure option.
- Lower prerequisite verison for autoconf to 2.53, and add missing functions in m4/. Add check for autoconf verison in bootstrap, and use m4 functions when needed.
- Change option '--with-mpi' to '--with-mpidir'
MEME version 3.5.0 -- September 15, 2005
This is the 12th year of MEME development. The current anniversary maintenance release for MEME contains a number of improvements to the installation and configuration of MEME/MAST servers and clients. Thanks to Nadya Williams of SDSC/NBCR for this work.
-
Refactoring of installation and configuration
- Restructure source directory tree to ease configuration.
- Highly simplified and optimized installation and configuration for MEME and MAST servers and clients using GNU autoconf/automake tools.
- Multiple configuration options available via arguments to "configure".
- Default installation of MEME, MAST server and clients, as well as the web site.
- Separate installatiion of server, client or web site if desired.
- Create a small test suite for 'make test'.
- Implement procedures for standard 'configure', 'make', 'make test', and 'make install'.
- Create scripts to run MEME/MAST servers as services, and automatically restarted them when physical host server reboots. Currenly, Linux and SunOS are supported.
- Simplified start of the servers with 'start-mast' and 'start-meme' scripts.
- Encapsulate site-specific variables in Globals.pm for perl scripts and in meme_config for sh scripts.
- Add csh and sh configuration scripts to set working environment.
- Availability as a Rocks Roll for integration with Rocks based cluster system.
-
Enhancements
- Sent MEME/MAST search results via an email as attachments, rather than inlined in the message body. This allows the MEME output to be saved properly for subsequent use with MetaMEME. It also reduces the chance of the output being modified by email filters.
- Check email addresses for entry accuracy using javascript. Thanks to Chris Misleh of NBCR for this feature.
- Check email addresses for valid domain names.
- Create new 'runtests' script to run all test suites. Simplify parsing of the output.
- Update FAQ(s) for MEME and MAST.
- Separate web-related files by type (html, cgi or image) and create a dir structure to support it. This simplifies web maintenace.
- Add examples of database and motif sequences files.
-
Known Issues
- The new meme and mast are binary executables, not shell scripts as they used to be.
When run with the appropriate arguments, they produce text (non-html) output. To get
the "old" behavior of meme and mast with the html output, use meme.csh and mast.csh
(without -text option). The following table gives new vs. old usage comparison.
old new meme myfile -dna -text > meme.res meme myfile -dna > meme.res # output will be a text file meme myfile -dna > meme.res meme.csh myfile -dna > meme.res # output will be an html file mast meme.res mast.csh meme.res # output will be an html file
- The new meme and mast are binary executables, not shell scripts as they used to be.
When run with the appropriate arguments, they produce text (non-html) output. To get
the "old" behavior of meme and mast with the html output, use meme.csh and mast.csh
(without -text option). The following table gives new vs. old usage comparison.
- Support Team Members Wilfred W. Li, Ph.D., Nadya Williams, M.S., Chris Misleh, and Tim Bailey, Ph.D.
MEME version 3.0.14 -- July, 2005
-
Bug Fixes
- an array out of bound error when MEME is run in parallel mode using certain DNA sequences with the "look for palindromes only" option enabled. Thanks to Tim Kaiser of SDSC/NBCR for the bug fix.
-
User Support
- all user questions are directed to our support team meme@nbcr.net.
MEME version 3.0 -- December, 2000
-
MEME enhancements
- Hypertext output: MEME now reports its output in hypertext (HTML) format with appropriate internal hot links among the results and the self-contained documentation on how to interpret them. The alignments are color-coded by nucleic acid or amino acid category.
- Direct MAST search: MEME motifs can now be used to search sequence databases using MAST simply by clicking on a button on the MEME HTML output document in an HTML-capable email reader or browser.
- Direct BLOCKS search: MEME motifs can now be submitted to the BLOCKS multiple alignment processor by clicking on a button on the MEME HTML output document in an HTML-capable email reader or browser. This allows MEME motifs to be converted to LOGOS or trees, and to be used to search other databases of motifs.
- New objective function: MEME searches for motifs that optimize the statistical significance of the log likelihood ratio of the occurrences of the motif.
- E-values: MEME computes and reports the statistical significance of motifs as the E-value of the log likelihood ratio. This provides an objective measure of how likely the motif is to be biologically significant.
- E-value stopping criterion: MEME will now stop when a motif whose E-value is above a user-given threshold is found. This guarantees that only motifs with a given E-value or better will be present in the output.
- Handling reverse complement DNA strands: MEME now handles reverse complement DNA strands correctly with all model types: OOPS, ZOOPS and TCM.
- Handling of ambiguous characters: MEME now handles ambiguous DNA and protein letters by converting them to the character "X". MEME treats the "X" character as "unknown", and correctly computes the probabilities of motif occurrences containing it.
- Higher-order background models: MEME now allows the user to specify a Markov model of arbitrary order via a file of tuple frequencies. This appears to improve the ability to discriminate between biologically interesting DNA motifs and motifs that are artifacts of the higher order statistics of DNA sequence.
- Multiple-alignment-based motif trimming: MEME defines a motif as a set of subsequences that can be correctly aligned without gaps. MEME can now trim the edges of motifs based on a local multiple alignment with gaps. MEME first determines the occurrences of the motif, then aligns each occurrence to the highest-scoring occurrence. These are combined into a multiple alignment, and MEME looks for a set of columns with no gaps. If a set of gapless columns at least <minw> wide is not found, MEME searches for a set with at most 1, 2, ... etc gaps until a set is found.
- Prior distribution on the number of occurrences: MEME now places a prior on the number of occurrences that controls how strong the bias towards motifs with a given number of sites is. Using a prior improves the performance of MEME with DNA, where the megaprior heuristic (used by default with protein sequences), is not applicable.
-
MAST enhancements
- Combining DNA strands: MAST now combines the score of a site in a DNA sequence with the score of the corresponding site on the reverse complement strand. (The final score for the site is the maximum of the two scores.)
- Scoring DNA strands separately: MAST still allows each strand of a DNA sequence to be treated as a separate sequence at the user's request.
- Ignoring reverse complement DNA: MAST also allows the user to score only the given DNA strand, not scoring the reverse complement strand at all.
- Background model: MAST now allows the user to specify the background residue frequencies used for computing E-values of scores.
- Composition-adjusted statistics: MAST can now use a different random model for each target sequence, based on the letter composition of that sequence. This can greatly reduce erroneous matches due to biased sequence compostion.
- New databases: The MAST website includes several new databases including "upstream" sequences for E. coli, B. subtilis and S. cerevesiae, and many complete genomes from GenBank.
-
MEME and MAST enhancements
-
MEME and MAST can be installed under the following operating systems:
- Mac OS X
- Linux (various manufacturers)
- SunSparc workstations (SunOS and Solaris operating systems)
- Decalpha workstations (OSF/1 operating system)
- Silicon Graphics workstations (IRIX version 5.3 operating system)
- Intel Paragon parallel computers
- Cray T3D parallel computers
- IBM SP (AIX operating system)
-
MEME and MAST can be installed under the following operating systems:
MEME version 2.2 -- February 25, 1998
-
MEME enhancements
- Sequence weights can be given in the input sequence file.
- The sites composing each motif are output in BLOCKS or FASTA format. BLOCKS format motifs can be converted to LOGOS, PSSMS and phylogeny trees using the Blocks Multiple Alignment Processor.
- A "negative" dataset may be specified causing the motifs to be optimized to discriminate between the training set family and the negative family. (This option is only available when you install MEME on your own computer.)
-
An advanced version of the MEME data submission form allows
- discovering palindromic DNA motifs,
- discovering motifs occurring on both DNA strands, and
- discovering more than ten motifs.
-
MAST enhancements
- DNA sequences (translated in six reading frames) can be searched using protein motifs.
- Hypertext (HTML) output including links to the ENTREZ database and improved motif diagrams are now output.
- Additional searchable databases added to the MAST website.
- The annotation section of output is smaller now since only regions in sequences where the motifs are present are printed.
- The ambiguous characters "*" and "-" are now permitted in motifs and sequence databases. They are treated as a single, unknown character in databases, and replaced by a weighted average of scores in motifs.
MEME version 2.1 -- March 25, 1997
-
Enhancements
- MAST output now includes measurements of similarities between all pairs of motifs in the query and a warning if any motifs are too similar. (Too similar motifs in a query can cause some p-values and e-values to be underestimated. These motifs can be removed from the query and MAST re-run to avoid the problem.)
- Cray T3E parallel computer now supported for MEME and MAST.
MEME version 2.0 -- October 17, 1996
-
Enhancements
- The output format of MEME has been improved to aid readability and user-friendliness.
-
MEME and MAST have been compiled and tested on:
- SunSparc workstations (SunOS and Solaris operating systems)
- Decalpha workstations (OSF/1 operating system)
- Silicon Graphics workstations (IRIX version 5.3 operating system)
- Intel Paragon parallel computers
- Cray T3D parallel computers
- MAST has been completely rewritten to provide more accurate p-values and to run significantly faster.
- A MAST server has been added to the MEME system website.
-
The MAST server lets you use the motifs found by MEME in your sequences
to search a wide variety of sequence databases including:
- nr (non-redundant protein and nucleotide databases)
- month (new or revised sequences in the last 30 days)
- swissprot (the last major release of the SWISS-PROT protein sequence database)
- genpept (protein translations from the GenBank feature table)
- dbest (expressed sequence tag database)
- dbsts (sequence tag site database)
- Several improvements have been made to the MEME website:
- You can now give the name of a file containing your sequences instead of having to cut-and-paste the sequences themselves.
- You may ask MEME to favor wide motifs instead of the (default) narrow motifs; this is especially useful with small sequence sets (fewer than 10 sequences.)
- The on-line documentation of MEME has been expanded and improved.
- MEME now determines the type of your sequences (PROTEIN or DNA) automatically.
- The MEME server now runs MAST on your sequences to make it easy for you to see the ordering and spacing of the motifs MEME discovered.
- NOTE and PROBER have been removed from the MEME system since their functionality is now superseded by MAST.
MEME version 1.4 -- February 29, 1996
-
Megaprior heuristic added to MEME.
- MEME now uses the megaprior heuristic with TCM models and the modified megaprior heuristic with ZOOPS models (by default). This greatly improves the sensitivity and selectivity of motifs using these types of models.
-
P-value computation added to MAST.
- MAST now computes p-values for sequences when searching large databases. This provides better discrimination between true and false positives than using z-scores. MAST is still only available via ftp, not via the web server.
- Various bug fixes to MEME.
MEME version 1.3 -- December 18, 1995
- MEME web server introduced!
- Various bug fixes to MEME.
MEME version 1.2 -- November 27, 1995
- MAST homology searcher introduced!
- MAST allows accurate homology searches of databases using motifs generated by MEME. The scores from all motifs characterizing a family are combined, normalized for sequence length, and sorted by z-score. The output of MAST is similar to that of BLAST, but, used in conjunction with MEME, MAST allows searching for sequences related to an entire family, not just a single sequence in the family. This provides better sensitivity and selectivity than single-sequence homology searches. MAST is currently only available in the ftp-able code, not via the web server.
- Various bug fixes to MEME.
MEME version 1.1 -- June 30, 1995
- Initial release of MEME, NOTE and PROBER.
Meta-MEME Release Notes
Release 3.3
-
The program
motif-scan
has been renamed tofimo
Release 3.x, Release 3.3, March 24, 2007
-
Added new tools:
- motif-scan
- Scans a database of sequences for the presence of motifs by calculating the p-value of the match to the motif at each position in the sequences.
- shadow
- Calculates the log-odds of a multiple alignment for a given phylogentic tree and evolutionary model at each position in the alignment.
- motiph
- Scans a multiple alignment for the presence of motifs by by calculating the p-values of motif-width windows in the alignment for a given phylogentic tree and evolutionary model.
- tom-tom
- Searches target motifs for elements similar to any in a set of query motifs.
-
Added
--global
option tomhmms
. This option causesmhmms
to score sequences using the best match between the model and the entire sequence. The default is to score using the best local match within a sequence. -
Added
--maxhits
option tomhmms
. This option sets an absolute limit to the number of hits returned bymhmms
. The default is to return all hits consistent with the E-value and p-value thresholds. -
Fixed error in
mhmms
that resulted in a sequence being considered a hit even if all positions were matched to a spacer state. -
Fixed error causing segmentation a fault in
mhmms
when the--motif-scoring
or--pthresh
options were used. -
Fixed error causing segmentation a fault in
mhmm
when the--order
option was used.
Release 3.21, August 3, 2005
- Modified meme-io.c to be able to parse the output from the latest versions of MEME.
- Modified the mcast script: removed the -allow-weak-motifs swich, and added the --keep-unused switch to the call to mhmm from mcast.
Release 3.2, October 7. 2004
- Reorganized source directory structure and implemented build system using autoconf and automake.
- Updated program documentation.
Release 3.1, February 4, 2004
- Remove the auxiliary program
score-n-store
. - Change command-line processing to follow POSIX.2 standard.
Release 3.0.1, June 2, 2003
- Add documentation for MCAST.
Release 3.0, May 15, 2003
- Remove
mhmmt
(EM training program) andmhmma
(multiple alignment program). - Add
mhmmscan
and themcast
wrapper program for searching DNA databases for regulatory modules. - Allow star topology in
mhmm
.