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),
PMID: 18978784
If you have questions or comments about this method/program please send a message to aje39 at cam dot ac dot uk and cei dot abreu at ed dot ac dot uk (science) or open an issue or discussion in this repository (code).
You'll need to have GSL (Gnu Scientific Library) installed on your system, version 1.11 or later. Version 1.10 is the first GSL version that contains the required hypergeometric functionality. However, it has a bug that may cause negative probabilities to be computed (as a result of computing the wrong tail). This bug was fixed for 1.11, which is by now an ancient version. In the Makefile, the variable GSLPREFIX needs to be set to the proper value. It should be such that
$(GSLPREFIX)/lib contains the GSL libraries (libgsl.a libgslcblas.a and/or
the .so variants of these).
$(GSLPREFIX)/include contains the GSL header files -- these will be in the
directory $(GSLPREFIX)/include/gsl
If, for some reason, on your system the GSL library files and header files do not share the same prefix as described above, make the necessary modifications in the Makefile -- it should be straightforward. After you have done this, typing 'make' should create a functioning sylamer executable.
By default the Makefile is set up such that the presence of zlib libraries on your system is assumed. Zlib enables Sylamer to read and write gzip-compressed files. The Makefile contains a brief description of what to do in case zlib is not on your system. Please note that it could be possible that zlib is on your system but for some reason not in the default include paths for your compiler. In that case, the solution is to provide the right include path and linker options to the compiler. Get in touch if you find yourself in this situation.
The manual page is available in HTML (sylamer.html), PDF (sylamer.pdf), PostScript (sylamer.ps), text format (sylamer.txt) and as a UNIX manual page (troff format, sylamer.1).
sylamer --help or sylamer -h
gives a synopsis of available options.