Posted by: shrikantmantri | November 5, 2009

MicroRazerS: Rapid alignment of small RNA reads.

via Bioinformatics on 11/3/09


Publication Date: 2009 Oct 29 PMID: 19880369
Authors: Emde, A. K. – Grunert, M. – Weese, D. – Reinert, K. – Sperling, S. R.
Journal: Bioinformatics

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.

post to: CiteULike

Posted via email from Sharing significant bytes —(Shrikant Mantri)

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