{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T14:47:01Z","timestamp":1761662821701},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability: MicroRazerS is part of the SeqAn C++ library and can be downloaded from http:\/\/www.seqan.de\/projects\/MicroRazerS.html.<\/jats:p>\n               <jats:p>Contact: \u00a0emde@inf.fu-berlin.de; grunert@molgen.mpg.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp601","type":"journal-article","created":{"date-parts":[[2009,10,31]],"date-time":"2009-10-31T00:13:10Z","timestamp":1256947990000},"page":"123-124","source":"Crossref","is-referenced-by-count":34,"title":["MicroRazerS: rapid alignment of small RNA reads"],"prefix":"10.1093","volume":"26","author":[{"given":"Anne-Katrin","family":"Emde","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, Free University of Berlin, Takustr. 9, 2 International Max Planck Research School for Computational Biology and Scientific Computing and 3 Group Cardiovascular Genetics, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany"},{"name":"1 Department of Computer Science, Free University of Berlin, Takustr. 9, 2 International Max Planck Research School for Computational Biology and Scientific Computing and 3 Group Cardiovascular Genetics, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany"}]},{"given":"Marcel","family":"Grunert","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Free University of Berlin, Takustr. 9, 2 International Max Planck Research School for Computational Biology and Scientific Computing and 3 Group Cardiovascular Genetics, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany"}]},{"given":"David","family":"Weese","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Free University of Berlin, Takustr. 9, 2 International Max Planck Research School for Computational Biology and Scientific Computing and 3 Group Cardiovascular Genetics, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany"}]},{"given":"Knut","family":"Reinert","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Free University of Berlin, Takustr. 9, 2 International Max Planck Research School for Computational Biology and Scientific Computing and 3 Group Cardiovascular Genetics, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany"}]},{"given":"Silke R.","family":"Sperling","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Free University of Berlin, Takustr. 9, 2 International Max Planck Research School for Computational Biology and Scientific Computing and 3 Group Cardiovascular Genetics, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany"}]}],"member":"286","published-online":{"date-parts":[[2009,10,29]]},"reference":[{"key":"2023012507524218600_B1","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/1471-2105-9-11","article-title":"SeqAn - an efficient, generic C++ library for sequence analysis","volume":"9","author":"D\u00f6ring","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023012507524218600_B2","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1038\/nbt1394","article-title":"Discovering microRNAs from deep sequencing data using miRDeep","volume":"26","author":"Friedl\u00e4nder","year":"2008","journal-title":"Nature Biotechnol."},{"key":"2023012507524218600_B3","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.0040022","article-title":"Exploration of small RNAs","volume":"4","author":"Kawaji","year":"2008","journal-title":"PLoS Genet."},{"key":"2023012507524218600_B4","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2008","journal-title":"Genome Biol."},{"key":"2023012507524218600_B5","doi-asserted-by":"crossref","first-page":"1966","DOI":"10.1093\/bioinformatics\/btp336","article-title":"SOAP2: an improved ultrafast tool for short read alignment","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012507524218600_B6","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1101\/gr.7179508","article-title":"Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells","volume":"18","author":"Morin","year":"2008","journal-title":"Genome Res."},{"key":"2023012507524218600_B7","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1089\/cmb.2006.13.296","article-title":"Efficient q-gram filters for finding all epsilon-matches over a given length","volume":"13","author":"Rasmussen","year":"2006","journal-title":"J. Comput. Biol."},{"key":"2023012507524218600_B8","doi-asserted-by":"crossref","first-page":"1646","DOI":"10.1101\/gr.088823.108","article-title":"RazerS - fast read mapping with sensitivity control","volume":"19","author":"Weese","year":"2009","journal-title":"Genome Res."},{"key":"2023012507524218600_B9","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1089\/10665270050081478","article-title":"A greedy algorithm for aligning dna sequences","volume":"7","author":"Zhang","year":"2000","journal-title":"J. Comput. 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