I received a mail informing me that TOUCAN, a regulatory sequence analysis package, just released a new version. More importantly, they've gone Open Source, which is good. I tried version 1.0 last year and had mixed feelings, notably about the Java interface. Version 2.0 brings lots of improvements on this side (the interface is still ugly, but its more functional), among other things. The feature set is impressive for anyone doing promoter regulation studies (automatic promoter retrieval, TRANSFAC database querying, overrepresentation analysis, etc). I pasted the announcement of the release, which include a changelog.
Dear TOUCAN user, Dear MotifSampler user, We are pleased to announce the second release of the TOUCAN software for cis-regulatory sequence analysis, and the 3.1 release of the MotifSampler algorithm. All information about TOUCAN can be found here: http://www.esat.kuleuven.ac.be/~saerts/software/toucan.php All information about MotifSampler can be found here: http://www.esat.kuleuven.ac.be/~thijs/Work/MotifSampler.html 1. Launching TOUCAN 2 Because you have entered your email adress before, you can now simply launch TOUCAN 2 by clicking here: http://www.esat.kuleuven.ac.be/~saerts/software/toucan.jnlp Or you can use your TOUCAN shortcut to version 1 (created by Java Web Start) if it is still on your desktop. This will automatically download the latest version. Note: this will only work if you have JAVA 2 and Java Web Start installed, see the web site for further information. 2. New Features in TOUCAN 2 Some of the new features in Release 2, since version 1.28.0, include: * ModuleScanner service: find the best N putative target genes of a cis-regulatory module in the genome (max_bp_length + a combination of PWMs as input). Returns top N sequences in a new window. This method is useful to validate a newly found module of the ModuleSearcher service. * Retrieve all Ensembl-available orthologous sequences for a set of genes automatically * New services added for sequence alignment: align 2 sequences with AVID, LAGAN (both global alignment) or BLASTZ (local alignment), and compare the results. * Align all orthologous pairs of sequences automatically in one job, using AVID, LAGAN, or BLASTZ. Ideally suited for sets of co-regulated genes. Then detect over-represented motifs in the conserved non-coding sequences. * Multiple alignment of an orthologous family by MLAGAN * Menu items have changed, for example all motif (transcription factor binding sites) related tools are grouped. * Zooming is improved: easy zooming by pressing Ctrl+ or Ctrl- * Faster sequence retrieval from Ensembl by omitting the retrieval of external references * After sequence retrieval from Ensembl, the "RevCompl Negatives" function reverse complements automatically all sequences that have the CDS on the negative strand. * Open/save files: remember the previously chosen directory Some of the new features that appeared gradually between the original publication in NAR and version 1.28.0 * FootPrinter 2.0 web service * ModuleSearcher web service, A* and GA version * Run MotifScanner on sublist sequences * JASPAR position weight matrices available * Automatic selection of features for all sequences 3. Open Source TOUCAN 2 has become open source software. By releasing the source code we hope that other people will contribute to the TOUCAN project, so that TOUCAN can provide - web services to all the latest algorithms (e.g., for multiple alignments, phylogenetic footprinting, binding site prediction, cis-module prediction, etc.) - better functionalities and visualizations - better integration with existing software or databases (e.g., genome browsers, DAS servers, etc.) - general robustness and ease-of-use, also for biologists If you would like to contribute to the project, please send me an email. Communications around the project can go via the mailing list (join here: http://listserv.cc.kuleuven.ac.be/cgi-bin/wa?SUBED1=toucan&A=1) 4. Service Mirrors We have prepared an installation package for the web services, so that they can be made available from other locations. We expect that this will increase the services uptime significantly. If you would also like to mirror the services, please send us an e-mail and we will forward you the installation instructions. All suggestions and comments are welcome and we hope you will find your cis-acting regions using TOUCAN ! Sincerely Yours, The TOUCAN Team. The MotifSampler Team.