Skip Navigation



Bioinformatics Advance Access published online on October 29, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp601
This Article
Right arrow Advance Access manuscript (PDF)
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Emde, A.-K.
Right arrow Articles by Sperling, S. R.
PubMed
Right arrow PubMed Citation
Right arrow Articles by Emde, A.-K.
Right arrow Articles by Sperling, S. R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

MicroRazerS: Rapid alignment of small RNA reads

Anne-Katrin Emde 1,2,*,{dagger}, Marcel Grunert 3,*,{dagger}, David Weese 1, Knut Reinert 1 and Silke R. Sperling 3

1 Department of Computer Science, Free University of Berlin, Takustr. 9, 14195 Berlin, Germany.
2 International Max Planck Research School for Computational Biology and Scientific Computing,Ihnestr. 73, 14195 Berlin, Germany.
3 Group Cardiovascular Genetics, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany.

*To whom correspondence should be addressed. Ms. Anne-Katrin Emde, E-mail: emde{at}inf.fu-berlin.de Marcel Grunert grunert{at}molgen.mpg.de


  Abstract

Motivation: 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 to other short read mapping tools. In addition, it is more sensitive and easy to handle and adjust.

Availability: MicroRazerS is part of the SeqAn C++ library and can be downloaded from http://www.seqan.de/projects/MicroRazerS.html.

Contact: emde{at}inf.fu-berlin.de, grunert{at}molgen.mpg.de

Associate Editor: Prof. Ivo Hofacker

{dagger} These authors contributed equally.

Received on June 19, 2009; revised on September 27, 2009; accepted on October 14, 2009

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.