Enright Lab: Sylamer | EMBL’s European Bioinformatics Institute Skip to main content Research Members Enright Lab: Sylamer Sylamer Fast assessment of microRNA binding and siRNA off-target effects from expression data Stijn van Dongen, Cei Abreu-Goodger & Anton J. Enright; Nature Methods(2008) A new online tool for running Sylamer on genelists is now available Sylarray. Sylamer is a system for finding significantly over or under-represented words in sequences according to a sorted gene list. Typically it is used to find significant enrichment or depletion of microRNA or siRNA seed sequences from microarray expression data. Sylamer is extremely fast and can be applied to genome-wide datasets with ease. Results are plotted in terms of a significance landscape plot. These plots show significance profiles for each word studied across the sorted genelist. To join the Sylamer mailing list please go to http://listserver.ebi.ac.uk/mailman/listinfo/sylamer-users This list is meant for general queries and bug reports in addition to receiving information about updates and bug-fixes. Software Java Graphical Interface This simple Graphical Interface is provided for convenience. Advanced usage of Sylamer is probably best performed using command-line binaries. Sylamer Java WebStart (RECOMMENDED) Java 1.5 JAR file Example Dataset The Java GUI contains precompiled binaries (see below) and should choose the appropriate one. You will need th R Statistical Package Installed for plotting results. Source Code & R scripts Information for compiling Sylamer on your own system Source code Precompiled Static Binaries Linux x86 Mac OSX (PPC) Mac OSX (x86) Windows (cygwin) Documentation Sylamer Manual Manual (HTML) Manual (PDF) Supplementary Data for Manuscript Genelists and UTRs used in the manuscript miR-155 knockout miR-430 injection RNAi Experiment
