Anne-Katrin Emde, Marcel Grunert, David Weese, Knut Reinert and Silke Sperling. MicroRazerS: rapid alignment of small RNA reads. Bioinformatics (2010) 26 (1): 123-124


Deep sequencing has become the method of choice for determining the small RNA content of a cell. Mapping the sequenced reads onto their reference genome serves as the basis for all further analyses, namely for identification and quantification. A look at current literature indicates that common short read mapping tools are suboptimal for the specific requirements of small RNA mapping. A method frequently used is Mega BLAST followed by several filtering steps, even though it is slow and inefficient for this task. MicroRazerS is a tool optimized for mapping short RNAs onto a reference genome. It is an order of magnitude faster than Mega BLAST, more sensitive and easy to handle and adjust. In addition, it is robust in the presence of sequencing errors and SNPs.

Main Features

  • supports Hamming distance read mapping with at most one error in seed
  • guarantees 100% sensitivity mapping for seed lengths 10 to 24
  • reads can be of arbitrary length and can contain adapter sequence at the 3' end

MicroRazerS Binaries

Supported platforms are at the moment Linux and Linux 64. Windows and Mac OS X will follow soon.

Version History


  • added support for seed lengths 10 to 24
  • added option -rr for recognition rate (mapping sensitivity)


  • first release of microRazerS using 16 as default seed length


For questions, comments, or suggestions feel free to contact Anne-Katrin Emde.


Last Update 4. March 2012