Release notes

Release 3.4 June 7, 2007,

• The program motif-scan has been renamed to fimo (find individual motif occurrences).
• tomtom assumed that pseudocounts had been applied in the MEME input file, and would generate a segmentation fault if any of the any of the position specific frequency matrix elements were 0. tomtom now defaults to a pseudocount of 1.0.

  tomtom, fimo, and motiph now share the same code for applying pseudocounts to the MEME input. At each position in the motif the nucleotide counts are generated by multiplying the number of sequences submitted to MEME by the elements of the position specific frequency matrix. The pseudocount is added to all the nucleotide counts and then the position specific frequency matrix is recalculated.

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 to mhmms. This option causes mhmms 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 to mhmms. This option sets an absolute limit to the number of hits returned by mhmms. 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) and mhmma (multiple alignment program).
• Add mhmmscan and the mcast wrapper program for searching DNA databases for regulatory modules.
• Allow star topology in mhmm.