Repository: Freie Universit├Ąt Berlin, Math Department

MicroRazerS: Rapid alignment of small RNA reads

Emde, A.-K. and Grunert, M. and Weese, D. and Reinert, K. and Sperling, S. R. (2010) MicroRazerS: Rapid alignment of small RNA reads. Bioinformatics, 26 (1). pp. 123-124. ISSN 1367-4803

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Official URL: http://bioinformatics.oxfordjournals.org/cgi/conte...

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@inf.fu-berlin.de, grunert@molgen.mpg.de

Item Type:Article
Subjects:Biological Sciences
Mathematical and Computer Sciences
Divisions:Department of Mathematics and Computer Science > Institute of Computer Science > Algorithmic Bioinformatics Group
ID Code:792
Deposited By: AG Alg BioInf
Deposited On:10 Nov 2009 13:22
Last Modified:01 Sep 2010 13:04

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