Last update: February 5, 2009
SPatt (Statistic for Patterns) is a suite of C++ programs designed for the computation of pattern occurrences p-value on text. Assuming the text is generated according to Markov model, the p-value of a given observation is its probability to occur. The lower is the p-value, the more unlikely is the observation. For example, this tools can be used to find patterns with unusual behaviour in DNA sequences.
If you want to learn more about SPatt, you might want to read about the statistics used in the package and/or consult our FAQ.
Want to see SPatt in action ? Please try it through WebSPatt our web interface to the package.
SPatt Version 1.3.1. Fixing some compilation issues and replaced GSL calls by more robust Rmath calls in cdf computations. SPatt 1.x now require the Rmath library (from the popular R software).
SPatt Version 1.3.0. Fixing some bugs and few lines of non free code.
SPatt Version 2.0-pre7. This a is a bug correction release.
It has been a long time since the last update of this website but SPatt is not dead ! Development of the 2.x branch continue and we publish SPatt Version 2.0-pre6. Here is a list of the features added since pre-1:
We are very proud to annonce the release of SPatt Version
2.0-pre1 the
first version of our new 2.x branch. This new branch
cannot yet completly replace the old 1.x branch since
many features have not yet been implemented. However, awesome
new specific features come with SPatt-2.0-pre1:
Release of SPatt Version 1.2.2. Many bug fixed and a new more reliable precise mode for ldspatt. Please note that this version should be one of the last of the 1.x branch. We will release soon the seed of our new DFA based 2.x branch.
Happy new year 2006 !! Here is a list of the upcoming features our team is currently working on:
New references added to the reference section. Important articles allowing to understand better the algorithms implemented in the package are available (in preprint version).
Release of SPatt-1.2.0 ! Main improvement concerns exact computations which are now done using Finite Markov Chain Imbedding (FMCI) techniques: higher reliability, less memory usage, and dramatically faster with degenerated patterns. Old exact computations using simple recurrences are still available with the oldxspatt program.
This website have one year, Happy Birthday ! To celebrate, let us release: SPatt-1.1.3. ldspatt is now capable to perform more precise computations with the "--precise" option.
SPatt-1.1.2 is out. Thanks to few C++ classes kindly provided by H. Richard, Markov order>0 and degenerate pattern support is now available for exact statistics. Few (minor) bugs have also been corrected.
Finally SPatt-1.1.1 is out. Huge Changelog on this release: major code revamp, new options (filtering and more), ldspatt up to 1000 times faster than before, xspatt 200 times faster than before ... a must have !
Moreover, WebSPatt our new web interface to SPatt is finally available with this release. Try it, enjoy, and do not hesitate to send us your feedback.
Our team is still working hard on the next release of SPatt. Highlighted upcoming features:
SPatt-1.0.9 is now available. A bug (again !) in xspatt have been discovered and corrected. The bug concerns exact statistics for highly overlapping words and should have in most cases few consequences on the computed statistics with version of xspatt prior to this one. An option allowing to filter sspatt output have been added. See ChangeLog for more details.
SPatt-1.0.8 is now available. Added support for all Markov models to cpspatt. Also added a statistic normalization option (see man page for more info). A static binary distribution is now available in the download section.
A comparison between SPatt and the EMBOSS wordcount program added in the benchmarks section.
Happy New Year !!
SPatt-1.0.7 is available. A minor bug have been discovered and corrected in X-SPatt. This concern only under-represented words occurring only once in the sequence.
A comparison of all program included in the package have been also added to the benchmarks section. Be sure to check it out.
SPatt-1.0.6 is out. A critical bug have been discovered and corrected in X-SPatt. All exact statistics computed with a prior version of SPatt should be considered with extreme care.
G-SPatt, a new program computing Gaussian statistics (only in the order 0 case for the moment) have been added to the package.
SPatt-1.0.5 is out. Few bugs fixed and new tests added for X-SPatt and CP-SPatt.
Due to a server migration, our web site was unreachable for the last 24 hours. We apologize for the inconvenience. Everything is now back to normal.
A new reference page have been added.
After weeks of heavy development, a new version of SPatt is out 1.0.4 ! In this release, many exciting features including two new statistical methods: exact statistics using simple recurrences (X-SPatt) and compound Poisson statistics (CP-SPatt). Please note that for the moment, these two programs are limited to order 0 Markov model and to non degenerate patterns.
SPatt 1.0 is out ! Large deviations statistics have been added (LD-SPatt).
A lot of minor changes that should improve the website.
SPatt 0.9 is out ! A critical problem in extreme under-represented statistics computations have been corrected.
Added comments in the benchmarks section.
Added a new benchmarks section. Check it out !
This web site goes on-line !