
Release notes
-
The program
motif-scan
has been renamed to
fimo
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 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
.