Enright Group : Sylamer

Fast assessment of microRNA binding and siRNA off-target effects from expression data

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.

You can download R here http://cran.wustl.edu/


• 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

• miR-155 knockout
• miR-430 injection
• RNAi Experiment