title: MicroRazerS: rapid alignment of small RNA reads.
abstract: BACKGROUND
  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 method frequently used is Mega BLAST followed by several filtering steps, even though it is slow and inefficient for this task. Also, none of the currently available short read aligners has established itself for the particular task of small RNA mapping.
  
  
  RESULTS
  We present MicroRazerS, a tool optimized for mapping small RNAs onto a reference genome. It is an order of magnitude faster than Mega BLAST and comparable in speed with other short read mapping tools. In addition, it is more sensitive and easy to handle and adjust.
  
  
  BACKGROUND
  MicroRazerS is part of the SeqAn C++ library and can be downloaded from http://www.seqan.de/projects/MicroRazerS.html.
authors.affiliation: Department of Computer Science, Free University of Berlin, Takustr. 9, Berlin, Germany. emde@inf.fu-berlin.de
authors.forename: Anne-Katrin
authors.initials: AK
authors.lastname: Emde
authors.forename: Marcel
authors.initials: M
authors.lastname: Grunert
authors.forename: David
authors.initials: D
authors.lastname: Weese
authors.forename: Knut
authors.initials: K
authors.lastname: Reinert
authors.forename: Silke R
authors.initials: SR
authors.lastname: Sperling
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D035683:MicroRNAs