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  MicroRazerS: rapid alignment of small RNA reads

Emde, A. K., Grunert, M., Weese, D., Reinert, K., & Sperling, S. R. (2010). MicroRazerS: rapid alignment of small RNA reads. Bioinformatics, 26(1), 123-124. doi:10.1093/bioinformatics/btp601.

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 Creators:
Emde, A. K.1, Author              
Grunert, M.2, Author              
Weese, D., Author
Reinert, K., Author
Sperling, S. R.3, Author
Affiliations:
1Gene Structure and Array Design (Stefan Haas), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479640              
2Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433550              
3Max Planck Society, ou_persistent13              

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Free keywords: Algorithms; Base Sequence; MicroRNAs/genetics; Molecular Sequence Data; Sequence Alignment/methods; Sequence Analysis, RNA/methods; *Software
 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 with 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.

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Language(s): eng - English
 Dates: 2010-01-01
 Publication Status: Published in print
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Title: Bioinformatics
Source Genre: Journal
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Pages: - Volume / Issue: 26 (1) Sequence Number: - Start / End Page: 123 - 124 Identifier: ISSN: 1367-4811 (Electronic) 1367-4803 (Linking) %R btp601 [pii] 10.1093/bioinformatics/btp601