MEME System Release Notes

MEME version 2.1 -- March 25, 1997

• 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

• The output format of MEME has been improved to aid readability and user-friendliness.
• MEME and MAST (Version 2.0) 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• NOTE and PROBER have been removed from the MEME system since their functionality is now superseded by MAST.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.